article{e9ac4e46-7f3f-4f79-aec3-ce5508715b29, abstract = {Comparative analysis of expressed sequence tags is becoming an important tool in molecular ecology for comparing gene expression in organisms grown in certain environments. Additionally, expressed sequence tag database information can be used for the construction of DNA microarrays and for the detection of single nucleotide polymorphisms. For such applications, we present PHOREST, a web-based tool for managing, analysing and comparing various collections of expressed sequence tags. It is written in PHP (PHP: Hypertext Preprocessor) and runs on UNIX, Microsoft Windows and Macintosh (Mac OS X) platforms.}, author = {Ahrén, Dag and Troein, Carl and Johansson, Tomas and Tunlid, Anders}, issn = {1471-8278}, language = {eng}, number = {2}, pages = {311--314}, publisher = {Wiley-Blackwell}, series = {Molecular Ecology Notes}, title = {PHOREST: a web-based tool for comparative analyses of expressed sequence tag data}, url = ...
Read "Large-scale EST sequencing in rice, Plant Molecular Biology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Sequencing of expressed sequence tags (ESTs) has been one of the primary techniques used for transcriptome analysis in a wide spectrum of species including those utilized for aquaculture. However, many researchers are still unfamiliar with the many genome applications and byprod- ucts of EST analysis, and they often regard ESTs as only short random sequences. Additionally, lack of cDNA library normalization, project planning, and quality control have often restricted the value of EST resources created in many laboratories. This review aims to address these issues by providing information on the construction of normalized cDNA libraries for efficient generation and analysis of ESTs and by highlighting the significance of EST analysis for the genome research of species lacking a sequenced genome. A successful EST project can provide the sequence tools needed for not only gene discovery, but also for physical, linkage and compara- tive mapping, analysis of alternative splicing and gene duplication, ...
Several methods have been developed for the comprehensive analysis of gene expression in complex biological systems. Generally these procedures assess either a portion of the cellular transcriptome or a portion of the cellular proteome. Each approach has distinct conceptual and methodological advantages and disadvantages. We have investigated the application of both methods to characterize the gene expression pathway mediated by androgens and the androgen receptor in prostate cancer cells. This pathway is of critical importance for the development and progression of prostate cancer. Of clinical importance, modulation of androgens remains the mainstay of treatment for patients with advanced disease. To facilitate global gene expression studies we have first sought to define the prostate transcriptome by assembling and annotating prostate-derived expressed sequence tags (ESTs). A total of 55000 prostate ESTs were assembled into a set of 15953 clusters putatively representing 15953 distinct transcripts.
Abstract Expressed sequence tags (ESTs) are complementary deoxyribonucleic acid (cDNA) fragments, which are reverse transcribed from mature ribonucleic acid (mRNA), a direct gene transcript. ESTs are a readily rich information source of complete expressed gene sequences. They reveal the type and number of genes being expressed in an organism. Joining ESTs into complete gene sequences is computationally expensive because they are numerous, erroneous, redundant and mixed up. ESTs that originate from the same gene are grouped together. This enables efficient consensus sequences generation, which reveals underlying gene sequences and their possible alternative splicings. EST clustering enables efficient discovery of expressed genes based on which several fields rely such as: disease diagnostics, drug discovery, genetic engineering, alternative splicing and many others. Most clustering algorithms developed so far are quadratic and their running time is prohibitively high. A tree-structured index ...
Isolation and sequence analysis of ZNRF2. The full-length cDNA sequence of human and mouse ZNRF2 was determined by analyzing expressed sequence tag (EST) clones (wh57e11, wi35c02, and xs53e14 for human; ux04e08, my52g11, and mu26f10 for mouse) obtained from the Washington University-Merck EST project. These clones were sequenced completely, and the sequence information was combined with those present in GenBank (Unigene clusters Hs.127294, Hs.209125, Hs.288088, Hs.300734, and Hs.351657 for human and Mm.423 and Mm.158534 for mouse) to create contiguous full-length sequences. Sequence editing, mapping, alignment, and contig production was performed using the DNASTAR (Madison, WI) and Vector NTI Suite 6 (InforMax, Frederick, MD) software packages. Human genome sequences for ZNRF1 and ZNRF2 were obtained from the database ( accession number AC099508 for ZNRF1; accession number AC006978 for ZNRF2) and compared with cDNA sequences of ZNRF1 and ZNRF2 using BLAST2 (basic local alignment search ...
BACKGROUND: Publicly accessible EST libraries contain valuable information that can be utilized for studies of tissue-specific gene expression and processing of individual genes. This information is, however, confounded by multiple systematic effects arising from the procedures used to generate these libraries. RESULTS: We used alignment of ESTs against a reference set of transcripts to estimate the size distributions of the cDNA inserts and sampled mRNA transcripts in individual EST libraries and show how these measurements can be used to inform quantitative comparisons of libraries. While significant attention has been paid to the effects of normalization and substraction, we also find significant biases in transcript sampling introduced by the combined procedures of reverse transcription and selection of cDNA clones for sequencing. Using examples drawn from studies of mRNA 3-processing (cleavage and polyadenylation), we demonstrate effects of the transcript sampling bias, and provide a
ul,,li,Preparation of EST data: Sequences were extracted from dbEST and were subjected to quality control screening (vector, E. coli, polyA, T, or CT removal, minimum length = 100 bp, < 3% N).,/li,,li,Preparation of transcript (ET) database: All sequences from the appropriate divisions of GenBank (including RefSeq) were extracted. Non-coding sequences were discarded and cDNAs and coding sequences from genomic entries were saved. Sequences and related information (e.g. PubMed links) are stored in the qcGene database (qcGene).,/li,,li,Assembly: Cleaned EST sequences and non-redundant transcript (ET) sequences were combined. Using the Paracel Transcript Assembler Program, sequences were assembled into contigs. TCs are consensus sequences based on two or more ESTs (and possibly an ET) that overlap for at least 40 bases with at least 94% sequence identity. These strict criteria help minimize the creation of chimeric contigs. These contigs are assigned a TC (Tentative Consensus) number. TCs may ...
PCR primers (forward, 5′ccgcacaccgactgggccaa3′; reverse, 5′gtcctcatgtargccttgtagt3′) were designed based on a conserved domain within synapsin 2 (syn2) mRNA sequences from several species in GenBank. Standard touchdown PCR reaction was performed with DNA from a zebra finch cDNA library (Holzenberger et al., 1997; Denisenko-Nehrbass et al., 2000) with annealing temperatures starting at 63°C minus 1° per cycle for eight cycles and 22 additional cycles at 55°C. The amplified product was excised from an agarose gel, eluted using Qiagen Gel Extraction kit, inserted into pPCRScript (Stratagene), and used to transform bacterial cells following standard procedures. Insert identity was confirmed by sequencing and analysis using DNAStar software. This amplified cDNA (GenBank accession number AY494948) (Fig. 1A) does not discriminate between the two syn2 isoforms. We also identified a set of expressed sequence tags (ESTs) representing syn2 from an EST collection derived from a normalized zebra ...
The DNATools sequencing software package version 5.1.375 is available for downloading at: http://www.crc.dk/phys/Dnatools/A01B04C04_Downloading.htm New in this revision: + Searching with protein strings on nucleotide sequences refined + File list based on Text Header content improved + Auto-build Text Headers after mail blast search improved + SAGE functions improved and thoroughly tested + Reporting facilities after SAGE tag file comparisons improved + Back-translation based on codon usage data now correct + Contig builder/editor improved (simple merge function) + Close redundant files improved (mostly for EST projects) + PSG (project subgroup) file handling improved DNATools is continuously being improved (as you may have noticed as a reader of this news group). This does not imply that upgrading is necessary each time a new revision is released. Im most cases the new revision only corrects minor bugs that you may not have noticed. My ambition, however, is to make bug fixes and improvements ...
Nygaard, V; Liu, Fang; Holden, Marit; Kuo, Winston P.; Trimarchi, Jeff; Ohno-Machado, Lucila; Cepko, Connie L.; Frigessi, Arnoldo; Glad, Ingrid K.; Wiel, Mark A. van de; Hovig, Eivind & Lyng, H (2008). Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics. ISSN 1471-2164. 9 . doi: 10.1186/1471-2164-9-258 Vis sammendrag Background Oligoarrays have become an accessible technique for exploring the transcriptome, but it is presently unclear how absolute transcript data from this technique compare to the data achieved with tag-based quantitative techniques, such as massively parallel signature sequencing (MPSS) and serial analysis of gene expression (SAGE). By use of the TransCount method we calculated absolute transcript concentrations from spotted oligoarray intensities, enabling direct comparisons with tag counts obtained with MPSS and SAGE. The tag counts were converted to number of transcripts per cell by assuming that the sum of all transcripts in a single ...
ESTviewer is a web application for interactively visualizing human gene structures, with emphasis on mammalian and avian expressed sequence tags (ESTs) that are conserved in the human genome and alternatively spliced (AS) variants. AS variants from the UCSC, Vega and PSEP annotations are presented in this application for comparison. EST data from six species, human, mouse, rat, cattle, pig and chicken, are mapped to the human genome to show cross-species EST conservation in annotated exonic and intronic regions. Cross-species EST conservation is evolutionarily and functionally important because it represents the effects of selection pressure on genic regions and transcriptome over evolutionary time. Emphatically, ESTviewer provides a convenient tool to compare highly conserved non-human ESTs and human AS variants. The application takes human gene accession Ids or coordinates of genomic sequences as inputs and presents annotated gene structures and their AS variants. In addition, the lengths and
In this study, we employed in silico analysis to identify a panel of marker genes for NSCLC prognosis and assessment of therapy efficacy. Based on our experimental results, the National Cancer Institute-Cancer Genome Anatomy Project database and the Digital Gene Expression Displayer program are useful tools for identifying differentially expressed genes between two pools of samples provided that a sufficient number of expressed sequence tags libraries for the tissue of interest are archived in the database. The differentially expressed genes can be further developed into marker genes for diagnostic or prognostic purposes by experimental verification procedures such as real-time qPCR.. NSCLC is heterogeneous with respect to histology and biological characteristics (15). Individual NSCLC cells within a tumor and in different patients tumors express different amounts of marker gene transcripts. The heterogeneity of marker gene expression levels in NSCLC cells limits the reliability of an assay ...
Usage: fossil tag SUBCOMMAND ... Run various subcommands to control tags and properties. fossil tag add ?OPTIONS? TAGNAME CHECK-IN ?VALUE? Add a new tag or property to CHECK-IN. The tag will be usable instead of a CHECK-IN in commands such as update and merge. If the --propagate flag is present, the tag value propagates to all descendants of CHECK-IN Options: --raw Raw tag name. --propagate Propagating tag. --date-override DATETIME Set date and time added. --user-override USER Name USER when adding the tag. --dryrun,-n Display the tag text, but do not actually insert it into the database. The --date-override and --user-override options support importing history from other SCM systems. DATETIME has the form YYYY-MMM-DD HH:MM:SS. fossil tag cancel ?--raw? TAGNAME CHECK-IN Remove the tag TAGNAME from CHECK-IN, and also remove the propagation of the tag to any descendants. Use the the --dryrun or -n options to see what would have happened. fossil tag find ?OPTIONS? TAGNAME List all objects that ...
AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been ...
The Pig Analysis Database presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed Sequence Tags (ESTs) generated by Sino-Danish Pig Genome Project, and 1 million miscellaneous GenBank records. The Pig Analysis Database has covered nearly 50% of the whole pig genome and over 70% of the coding sequences (CDS), and aims to provide the most complete pig gene set to date.. In addition to gene annotations, the Pig Analysis Database also presents expressional information from 98 EST libraries, SNPs detected from both WGS reads and ESTs, oligos that can be used in microarray design and relevant evolutionary data.. Various views can be found here.. ...
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23. PMID: 19498102; PMC: PMC2704439 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 ...
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23. PMID: 19498102; PMC: PMC2704439 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 ...
STACK_PACK EST CLUSTERING MANAGEMENT AND ANALYSIS TOOL-SUITE now available SANBI announces the free academic availability of the STACK_PACK EST clustering management and analysis tool-suite. STACK_PACK 1.0 has been developed by SANBI in collaboration with Electric Genetics, Cape Town (PTY) LTD, to support analysis of the increasing EST load for Gene Discovery. The tool-suite interchangeably supports modules such as PHRAP and other assemblers, and includes D2-cluster and CRAW together with other codes specifically developed for the system. STACK_PACK manages flow and stringent analysis of data between these applications. The system creates two outputs: a standard data set as well as a more highly-qualified data subset based upon consensus quality. Alternate splicing and low quality EST consensi are also detected and processed. This system has been used to manufacture STACK, the sequence tag alignment and consensus knowledgebase which is also distributed by SANBI. ...
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brain, neuroblastoma, non-normalized, cell line, EST, unknown developmental stage, MGC, Rubin non-normalized, size fractionated, plasmid vector, directionally cloned, oligo-dT ...
There is no tag wiki for this tag … yet! Tag wikis help introduce newcomers to the tag. They contain an overview of the topic defined by the tag, along with guidelines on its usage. All registered users may propose new tag wikis. (Note that if you have less than 20000 reputation, your tag wiki will be peer reviewed before it is published.) ...
There is no tag wiki for this tag … yet! Tag wikis help introduce newcomers to the tag. They contain an overview of the topic defined by the tag, along with guidelines on its usage. All registered users may propose new tag wikis. (Note that if you have less than 20000 reputation, your tag wiki will be peer reviewed before it is published.) ...
There is no tag wiki for this tag … yet! Tag wikis help introduce newcomers to the tag. They contain an overview of the topic defined by the tag, along with guidelines on its usage. All registered users may propose new tag wikis. (Note that if you have less than 20000 reputation, your tag wiki will be peer reviewed before it is published.) ...
There is no tag wiki for this tag … yet! Tag wikis help introduce newcomers to the tag. They contain an overview of the topic defined by the tag, along with guidelines on its usage. All registered users may propose new tag wikis. (Note that if you have less than 4000 reputation, your tag wiki will be peer reviewed before it is published.) ...
Lib=934[Homo_sapiens,prostate,prostatic_intraepithelial_neoplasia_- _high_grade,,,adult] Length=234 Length = 234 Plus Strand HSPs: Score = 156 (23.4 bits), Expect = 1.4, P = 0.76 Identities = 82/128 (64%), Positives = 82/128 (64%), Strand = Plus / Plus Query: 225 TGGGAATAAAATT-CTA-AGTGAATACATAAAGAAATTAAAAGAAACTACAGNATCATTA 282 TGG AA AA ATT CT A TG TACATAAAGAAATT A GAAA T AT TT Sbjct: 76 TGGTAACAACATTTCTTCAATGT-TACATAAAGAAATTGAGGGAAATTTTGCAATACTTG 134 Query: 283 AGATTACCAAAATTTA-CATGGACAACTA--CACTTG-ATCTTGTGCAAACATCGACATC 338 G TTACC TTTA C TGGACA A CACT G AT T GC AC T G CA C Sbjct: 135 GGGTTACCTT--TTTATCTTGGACAGTGATCCACTAGTATATCAGGCTGACCTAGTCAAC 192 Query: 339 TA-TGGGTATT 348 T TGG TATT Sbjct: 193 TGGTGGCTATT 203 cbil,dbest,162347">>cbil,dbest,162347 T92226 ye17e11.r1 5 Lib=249[Homo_sapiens,lung,,,,72_years] Length=245 Length = 245 Plus Strand HSPs: Score = 146 (21.9 bits), Expect = 4.6, P = 0.99 Identities = 54/80 (67%), Positives = 54/80 (67%), Strand = Plus / Plus Query: 212 ...
Lib=9[Plasmodium_falciparum,,,,,] Length=346 Length = 346 Plus Strand HSPs: Score = 184 (27.6 bits), Expect = 0.028, P = 0.028 Identities = 130/206 (63%), Positives = 130/206 (63%), Strand = Plus / Plus Query: 22 TTACA-ATATTTTGTGAATAAACTTTTTGGTGATTTGCCATCAAGTTTTAATTATATGAT 80 TTA A AT TTTTGTGA T A TT TG T TG A AAG AATT T GA Sbjct: 4 TTATACATCTTTTGTGATTTAGGTTAAAA-TG-TATGTTA--AAGAAGAAATTGTG-GAG 58 Query: 81 -AGGCAAAACGATA-GAG-T-ATGA-TATAAAGATTAGTTATTATGAAATATATGAAGGG 135 A G AAAAC AT GA T AT A TA AAAGA AG A AT AAATATATGAA GG Sbjct: 59 GAAGAAAAACTATCTGATATTATCAATAAAAAGAA-AGAAAACATAAAATATATGAAAGG 117 Query: 136 CATGNTAAAAATGGTGAAGAGGTTTGTGT-ATTT-ATATATGAGAAGAA--TAATAAAGA 191 ATG AAAA T TGAA A TT G ATTT A A TGA A GAA TA T A GA Sbjct: 118 AATG--AAAATTCCTGAAAATATTCTAGCCATTTCAAACTTGA-AGGAAGTTATTGATGA 174 Query: 192 AACGAGTTTTGTAAAANGATATATAAA-ACNCCATT 226 C AG TTTGT AA T TAT A AC CCA T Sbjct: 175 TGC-AGATTTGTTAATATTTGTATTACCACACCAAT 209 cbil,dbest,1133595">>cbil,dbest,1133595 AA488925 aa55b10.r1 5 ...
Hi i have created several div tags and the corresponding css ids and am having a problem with creating a final tag that will house 3 individual div tags. the problem tag is the #selection tag. i...
In gene expression when exposed to CO2 elevated to 560 mmolmol21. The expression of 4600 expressed sequence tags in poplar have been investigated by Gupta et
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If most combinations build by following Thursday, the testing-next branch is merged to the testing branch. Regardless, the repository is tagged with the tested_YYYY-MM-DD tag. An annotated tag is used with a message that includes a text copy of the above table with variations that have been tested building for this cycle. The reason we tag after testing is complete is so that we can include status in the annotated tag. This way information about what was tested with each tagged version is captured in the repository. A link is added for easy reference to the log below ...
If most combinations build by following Monday, the testing-next branch is merged to the testing branch. Regardless, the repository is tagged with the testing_YYYY-MM-DD tag. An annotated tag is used with a message that includes a text copy of the above table with variations that have been tested building for this cycle. The reason we tag after testing is complete is so that we can include status in the annotated tag. This way information about what was tested with each tagged version is captured in the repository. A link is added for easy reference to the log below ...
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Advertised routes are associated with a particular tag in a routing database in a second router. A first router subsequently sends one or more messages associated with a route withdraw operation that
Hi I know alt tags should be on an image, however at the moment I have 15,800 missing on the site, how important are these? Its a big project for...
Hope you win!, you're currently the high bidder, but you're close to getting outbid., this auction is almost over and you're currently the high bidder., you're the high bidder, but. Tags: bts, summer, package, buy. ...
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... - I asked the exact same thing on the knitting page, but thought id ask both:My mom and I are crocheting all the yarmulkes for my wedding. But we
FamousFeatures is a free intermediary service for people wishing to sell a story to the press. We adhere to the IPSO (Independent Press Standards Organisation) code of practice ...
Its a lot more workable to run your skin care business when you have an easy to understand image of where you want to take it. For you to fulfill all the goals you have, you have to get rid of numerous challenges that come your method. The standards listed below might assist you in broadening and m… Read more ...
Its a lot more workable to run your skin care business when you have an easy to understand image of where you want to take it. For you to fulfill all the goals you have, you have to get rid of numerous challenges that come your method. The standards listed below might assist you in broadening and m… Read more ...
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FamousFeatures is a free intermediary service for people wishing to sell a story to the press. We adhere to the IPSO (Independent Press Standards Organisation) code of practice ...
安装了星空急速的所有用户均被这个软件记录下并发回了MAC地址,保守估计我国星空极速比较普及的某省份要有50%的MAC地址被这款软件绑定, 我们要关注的是,随之而来的将是什么 ...
2017諾貝爾獎證實中醫兩千年前的養生論三位研究「晝夜節律的分子運作機制」的科學家Jeffrey C. Hall、Michael Rosbash和Michael W. Young獲得了2017諾貝爾生理學和醫學獎。晝夜節律是由體內的「生物鐘」操控的,它可以測到白天和夜晚的循環,將生理功能調整到最佳狀態。如果人們的...
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You will be able to search Sagittarius names now by months (Either November/December) through tags and categories. Being updated daily. - RindaDi (2018). ...
You will be able to search Sagittarius names now by months (Either November/December) through tags and categories. Being updated daily. - RindaDi (2018). ...
Tags: Αγγεία.με.μονόδρομη.ροή-Χαρακτηριστικά Αδένας.δράσης.ορμόνης Αδένας.εγκεφάλου-Παραγόμενη.ορμόνη Βιολογική.σημασία.υγρού Είδη.αγγείων Είδος.μεταφερόμενων.μηνυμάτων Θηλασμός-Εκκρινόμενο.γάλα Κατανομή.φαιάς-λευκής.ουσίας.νωτιαίου.μυελού Όργανα.Κεντρικού.Νευρικού.Συστήματος Περιεχόμενο.υγρό Πολυπληθέστερα.και.λεπτότερα.αγγεία-Ρόλος Σύσταση.φαιάς-λευκής.ουσίας Τμήμα.εγκεφάλου Υποδοχείς.μαστών Χώροι.κυκλοφορίας. ...
The public EST (expressed sequence tag) databases represent an enormous but heterogeneous repository of sequences, including many from a broad selection of
Transcriptome analysis can provide useful data for refining genome sequence annotation. Application of massively parallel signature sequencing (MPSS) revealed reproducible transcription, in multiple MPSS cycles, from 73% of computationally predicted genes in the Theileria parva schizont lifecycle stage. Signatures spanning consecutive exons confirmed 142 predicted introns. MPSS identified 83 putative genes, , 100 codons overlooked by annotation software, and 139 potentially incorrect gene models (with either truncated ORFs or overlooked exons) by interfacing signature locations with stop codon maps. Twenty representative models were confirmed as likely to be incorrect using reverse transcription PCR amplification from independent schizont cDNA preparations. More than 50% of the 60 putative single copy genes in T. parva that were absent from the genome of the closely related T. annulata had MPSS signatures. This study illustrates the utility of MPSS for improving annotation of small, gene-rich ...
Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR.
dbEST is a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or ...
Citation: Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Chingcuanco, D.L., Hayden, D.M., Donze, T., Vivia-Lindsay, A., Stamova, B., Coleman-Derr, D. 2006. EST sequencing and phylogenetic analysis of the model grass brachypodium distachyon. Theoretical and Applied Genetics. 113: 186-195. Interpretive Summary: Brachypodium distachyon is a small grass that serves as a model system for the temperate grasses (i.e. forage grasses and cereals). Expressed sequence tags (ESTs) are short DNA sequences from random cDNAs (genes). ESTs are useful tools for many functional and physical genomic experiments including the construction of microarrays and the development of molecular markers. This paper describes the sequencing of a large collection of ESTs from five different cDNA libraries. Analysis of the ESTs included the identification of putative lignin biosynthetic genes and the construction of phylogentic trees that demonstrated the close relationship of Brachypodium to wheat and barley. Technical ...
Despite advances in sequencing technology, we are still a long way from having well-annotated genome sequences for all organisms of interest. Instead, EST (Expressed Sequence Tag) data is available for less popular organisms in many cases, prior to a genome project. EST data presents a particular challenge for the identification of proteins using mass spectrometry (MS): it is often redundant (multiple copies of the same gene), consists primarily of short fragments of coding sequence, contains many sequencing errors and is generally poorly annotated. Nevertheless, generating EST libraries represents a much cheaper alternative to full genome sequence and has the advantage of focusing on the parts of the genome of interest to proteomics, i.e. the expressed genes, many of which will be protein-coding. The School of Biological Sciences, Centre for Proteomic Research and the National Oceanography Centre, Southampton have been collaborating to develop bioinformatics analysis tools to help clean up the ...
In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination. The identification of ESTs has proceeded rapidly, with approximately 74.2 million ESTs now available in public databases (e.g. GenBank 1 January 2013, all species). An EST results from one-shot sequencing of a cloned cDNA. The cDNAs used for EST generation are typically individual clones from a cDNA library. The resulting sequence is a relatively low-quality fragment whose length is limited by current technology to approximately 500 to 800 nucleotides. Because these clones consist of DNA that is complementary to mRNA, the ESTs represent portions of expressed genes. They may be represented in databases as either cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand. One can map ESTs to specific chromosome locations using physical mapping techniques, such as ...
Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value | 10-5) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified
At PlantGDB, efforts are undertaken to identify and remove all contaminant DNA so that a clean dataset is made available to researchers. Here, we use the Vmatch program (with options -l 50 -identity 90) to screen EST sequences against UniVec for vector contaminations as well as against E. coli genomes for bacterial sequences contaminations. The table lists the individual contaminated sequence. (Return to Vector Contamination menu). ...
1 #include ,graphics.h, 2 3 #include ,iostream.h, 4 #include ,math.h, 5 #include ,dos.h, 6 #include ,conio.h, 7 8 void main( ) 9 { 10 float x, y, x1, y1, x2, y2, dx, dy, step; 11 int i, gd = DETECT, gm; 12 initgraph(&gd, &gm, C:\\TURBOC3\\BGI); 13 14 cout ,, Enter the value of x1 and y1 : ; 15 cin ,, x1 ,, y1; 16 cout ,, Enter the value of x2 and y2: ; 17 cin ,, x2 ,, y2; 18 19 dx = (x2 - x1); 20 dy = (y2 - y1); 21 if(abs(dx) ,= abs(dy)) 22 step = abs(dx); 23 else 24 step = abs(dy); 25 dx = dx / step; 26 dy = dy / step; 27 x = x1; 28 y = y1; 29 i = 1; 30 while(i ,= step) { 31 putpixel(x, y, 5); 32 x = x + dx; 33 y = y + dy; 34 i = i + 1; 35 delay(100); 36 } 37 getch(); 38 closegraph(); 39 } ...
Major recent improvements in biotechnology have led to an accelerated production of DNA sequences. The completion of the human genome sequence, along with the genomes of more than two hundred other species, has marked the arrival of the genome era. The ultimate goal is to understand the structure and function of genomes and their genes. This thesis has focused on the computational analysis of complementary DNA (cDNA) sequences. These are copies of mRNA transcripts that correspond to the coding regions of genomes.. Studying the expression patterns of genes is essential for understanding gene function. Many gene expression profiling techniques generate short sequence tags that derive from transcripts. A pilot study was performed to assess the feasibility of using the pyrosequencing platform for gene expression analysis. The sequences generated by pyrosequencing in most cases (≈ 85%) were long enough (, 18 nucleotides) to uniquely identify the corresponding transcripts through database searches. ...
Animals and Treatments. All animal experiments and treatments were reviewed and approved by the Research Animal Resource Center at the University of Wisconsin or by the appropriate oversight department of submitting institutions. Institutions, strains, sex, ages, treatment vehicle, circadian time, and route of administration are recorded for all experiments and can be found for each experiment at the EDGE Web site.. Expressed Sequence Tag Libraries. Poly-A mRNA was isolated from total RNA via the Oligotex kit (QIAGEN, Valencia, CA). Construction of expressed sequence tag (EST) libraries was typically performed by using the cDNA Timesaver kit (Amersham Biosciences Inc., Sunnyvale, CA). In brief, 5 μg of poly-A was used to generate first strand cDNA with an anchored poly-T oligonucleotide [dT(18)-N] that also contained a NotI-specific restriction site. First strand cDNA was then purified via a phenol/chloroform extraction. After second strand synthesis, cDNA was again purified using ...
abstract = {A novel mosquito antimicrobial peptide, gambicin, and the corresponding gene were isolated in parallel through differential display-PCR, an expressed sequence tag (EST) project, and characterization of an antimicrobial activity in a mosquito cell line by reverse-phase chromatography. The 616-bp gambicin ORF encodes an 81-residue protein that is processed and secreted as a 61-aa mature peptide containing eight cysteines engaged in four disulfide bridges. Gambicin lacks sequence homology with other known proteins. Like other Anopheles gambiae antimicrobial peptide genes, gambicin is induced by natural or experimental infection in the midgut, fatbody, and hemocyte-like cell lines. Within the midgut, gambicin is predominantly expressed in the anterior part. Both local and systemic gambicin expression is induced during early and late stages of natural malaria infection. In vitro experiments showed that the 6.8-kDa mature peptide can kill both Gram-positive and Gram-negative bacteria, has ...
Multimeric protein complexes have a role in many cellular pathways and are highly interconnected with various other proteins. The characterization of their domain composition and organization provides useful information on the specific role of each region of their sequence. We identified a new module, the PAM domain (P CI/PINT a ssociated m odule), present in single subunits of well characterized multiprotein complexes, like the regulatory lid of the 26S proteasome, the COP-9 signalosome and the Sac3-Thp1 complex. This module is an around 200 residue long domain with a predicted TPR-like all-alpha-helical fold. The occurrence of the PAM domain in specific subunits of multimeric protein complexes, together with the role of other all-alpha-helical folds in protein-protein interactions, suggest a function for this domain in mediating transient binding to diverse target proteins.
EST). A short partial sequence, typically 200-400 bp long, of a complementary DNA (cDNA) clone. Because cDNAs are prepared by reverse transcription of messenger RNA molecules, ESTs act as markers for genes that are expressed in particular tissues or organs. EST sequence data are held on databases, and researchers use computer programs to search for sequences that correspond to, say, a partial amino-acid sequence for a protein under investigation. The EST sequence can then be used to construct a DNA probe to locate the respective clone from a DNA library. ...
Hsiang, T. and P.H. Goodwin. 2003. Distinguishing plant and fungal sequences in ESTs from infected plant tissues. Journal of Microbiological Methods 54:339-351. Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant database is larger and therefore one would presume that BLASTX analysis of it would be more accurate, superior resolution of 700 randomly selected fungal ESTs was found with Standalone TBLASTX analyses with a local matching database composed of a plant and a fungal genome. Standalone TBLASTX analyses of 3983 ESTs from nine different fungal-infected plant EST libraries also proved to be superior in identifying the origin of sequences as either plant or fungal compared to GenBank BLASTX analysis. Standalone TBLASTX with a matching database comprised of a single ...
De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
p,Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.,/p,,p,The ,a href=https://genome.ucsc.edu/cgi-bin/hgc?hgsid=423831555_sqRhAapgi8atmzzBPBAz8Me5797J&c=chr14&o=94517268&t=94547548&g=wgEncodeGencodeCompV19&i=ENST00000544005.1#tsl target=_self,Transcript Support Level,/a, (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.,/p,TSL:1The GENCODE set is the gene set for human and mouse. ,a href=/Help/Glossary?id=500 class=popup,GENCODE Basic,/a, is a subset of representative transcripts (splice variants).GENCODE basic,p,PRINCIPAL1 - APPRIS candidate principal isoform.,/p,,p,,a class=popup href=/Homo_sapiens/Help/Glossary?id=521,APPRIS,/a, is a system to annotate alternatively spliced transcripts based on a range of computational methods.,/p,APPRIS P1 ...
ARTICLE. Ayoubi P, Jin X, Leite S, Liu X, Martajaja J, Abduraham A, Wan Q, Yan W, Misawa E and Prade R 2002 PipeOnline 2.0: Automated EST Processing and Functional Data Sorting Nucleic Acid Research 30: 4761-4769. Expressed sequence tags (ESTs) are generated and deposited in the public domain, as redundant, un-annotated, single-pass reactions, with virtually no biological content. PipeOnline automatically analyses and transforms large collections of raw DNA-sequence data from chromatograms or FASTA files by calling the quality of bases, screening and removing vector sequences, assembling and rewriting consensus sequences of redundant input files into a unigene EST data set and finally through translation, amino acid sequence similarity searches, annotation of public databases and functional data. PipeOnline generates an annotated database, retaining the processed unigene sequence, clone/file history, alignments with similar sequences, and proposed functional classification, if available. ...
p,Transcript Support Level 1, when transcripts are supported by at least one non-suspect mRNA.,/p,,p,The ,a href=https://genome.ucsc.edu/cgi-bin/hgc?hgsid=423831555_sqRhAapgi8atmzzBPBAz8Me5797J&c=chr14&o=94517268&t=94547548&g=wgEncodeGencodeCompV19&i=ENST00000544005.1#tsl target=_self,Transcript Support Level,/a, (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.,/p,TSL:1The GENCODE set is the gene set for human and mouse. ,a href=/Help/Glossary?id=500 class=popup,GENCODE Basic,/a, is a subset of representative transcripts (splice variants).GENCODE basic,p,PRINCIPAL1 - APPRIS candidate principal isoform.,/p,,p,,a class=popup href=/Homo_sapiens/Help/Glossary?id=521,APPRIS,/a, is a system to annotate alternatively spliced transcripts based on a range of computational ...
All ESTs in GenBank on the date of the track data freeze for the given organism are used - none are discarded. When two ESTs have identical sequences, both are retained because this can be significant corroboration of a splice site.. ESTs are aligned against the genome using the Blat program. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within a selected percentage of the best are kept. Alignments must also have a minimum base identity to be kept. For more information on the selection criteria specific to each organism, consult the description page accompanying the EST track for that organism.. The maximum intron length allowed by Blat is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. If an EST aligns non-contiguously (i.e. an intron has been spliced out), it is also a candidate for the Spliced EST track, provided it meets various quality ...
The high frequency of alternative splicing among plant Serine/Arginine-rich (SR) family of proteins has been linked to important roles in gene regulation during development and in response to environmental stress. In this report, the genomes of maize and sorghum have been searched and the manual annotation of all the SR proteins have been performed. The experimental validation of gene structure by RT-PCR analysis revealed, with few exceptions, that SR genes produced multiple isoforms of transcripts by alternative splicing. Despite sharing high structural similarity and conserved positions of the introns, alternative splicing profiles of vast majority of SR genes are not conserved between maize and sorghum. These include many transcript isoforms discovered by RT-PCR and not represented in extant EST collection. The occurrence of several isoforms of maize and sorghum SR mRNAs have been determined and that these isoforms display evolutionary conservation of splicing events with their homologous SR ...
Global Animal Tag Supplier Directory, Animal Tag, Animal Tag Manufacturers, Animal Tag Factories, Animal Tag Manufacturing, Animal Tag Manufacturer, Factory,Animal Tag Export Company, Animal Tag Suppliers, Exporters, Animal Tag Producers, Wholesalers, Distributors, International Animal Tag, OEM Animal Tag, Agriculture.
Global Animal Tag Supplier Directory, Animal Tag, Animal Tag Manufacturers, Animal Tag Factories, Animal Tag Manufacturing, Animal Tag Manufacturer, Factory,Animal Tag Export Company, Animal Tag Suppliers, Exporters, Animal Tag Producers, Wholesalers, Distributors, International Animal Tag, OEM Animal Tag, Agriculture.
Transcriptome profiling and digital gene expression are tewo examples that illustrate the power of NGS. For a few thousand dollars, a single run of a SOLiD or Illumina sequencer can produce more ESTs (Expressed Sequence Tags) than exist in all of dbEST. Even more striking is that the data in dbEST were collected over many years and 100s million dollars were invested in getting the sequences. Also, it is important to understand that the data in dbEST represent only a relatively small number of molecules from a broad range of organisms and tissues. While dbEST has been useful for providing a glimpse into the complex nature of gene expression and, in the case of human, mouse and a few other organisms, mapping a reasonable number of genes, the resource is unable to provide the deeper details and insights into alternative splicing, antisense transcription, small RNA expression, and allelic variation that can only be achieved when a cells complement of RNA is sampled deeply. As recent literature ...
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You can often find vector information at NCBI, either directly or in their list of vectors screened for contamination of new sequence at Vecscreen. VectorDB contains information about many common vectors, including yeast vectors. The EMBL Hamburg outstation maintains a large database of vectors. I.M.A.G.E. Consortium Vectors contains information about plasmids commonly used in EST collections such as those sold by OpenBioSystems and Invitrogen. For eukaryotic vectors (Fish, Xenopus) see Minnesota. The Forsburg Lab maintains a list of Fisson Yeast vectors. Promega maintains a list of their vectors. NEB maintains a list of common vectors. Epicentre also maintains its own list. Lucigen provides transcription-free vectors for cloning AT-rich and other difficult DNAs. Addgenes Vector DB contains most of the information from Stanfords VectorDB, plus more vector information they have curated from commercial websites and added through our plasmid curation efforts. (However, it seems to be rather ...
After switching from Preview to Show All Tags view composer has what appears to be a second body tag (actually a graphic relic) showing in the show all tags view. Build: 2001091003 Reproducibility: Everytime Steps to Reproduce: 1.Open Composer 2.Switch to Preview view 3.Switch to Show All Tags view Actual Results: A second body tag will appear to show up behind the real one. This is not a real body tag but something that appears there. Expected Results: I would expect that only one body tag would appear no matter what view I switch from ...
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Cest en janvier 2012 que lincontournable Lana del Rey a pris possession de lindustrie avec Born To Die annoncé en grandes pompes par le féérique Video Games. Dune harpe diablement envoutante, une instrumentale dune fragilité stupéfiante, une voix percutante de sensibilité, des textes très bien choisis et un charme dinterprétation hors norme, est né un tube européen assurément proche de la perfection. Un titre plus que prometteur donc pour cette américaine qui ne déçoit cependant pas : lopus est en effet à la hauteur des espérances. Son ouverture est assurée par le titre éponyme qui dresse remarquablement la couleur dominante de lopus. La production épurée à lextrême sous une voix fine, impudente et poignante de nonchalance offre indubitablement limage dune reine régnant sur le triste trône de la vie, dont la majesté exacerbée par le clip vidéo nous présente réellement le personnage. On est tenu et transporté jusquà la dernière seconde dans son ...
The question arises, "So how are tags different from categories?" Well, they arent really very different, except in terms of flexibility. The thirty or so categories Ive established for this blog are pretty much set, and I dont add a new category lightly. I establish a category only when I figure I will write something in that vein repeatedly. Categories are an inherently more conservative scheme. Tags are fast and loose, and they proliferate like vermin. With tags Ive tried to err in the other direction, so many tags may be used only once and never show up again. Categories are restrictive and clean. Tags are expansive and messy. In fact they way theyre implemented in WordPress tags seem to encompass and include categories, which makes a certain amount of sense. Theyre both simply schemes for sorting through information. Of course tags are more powerful when implemented a true folksonomy but this blog is a solo project, not a collaborative effort.. So how many do I have so far? Lets see. ...
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RH_TOPICTAGS_SEARCH_HEADER_ANY =, Search for topics with any of these tags: %s, RH_TOPICTAGS_SEARCH_HEADER_ALL =, Search for topics with all of these tags: %s, RH_TOPICTAGS_NO_TOPICS_FOR_TAG_ANY =, There are no topics tagged with any of these tags: %s, RH_TOPICTAGS_NO_TOPICS_FOR_TAG_ALL =, There are no topics tagged with all of these tags: %s ...
Incorrectly tagged questions are hard to find and answer. If you know of common, alternate spellings or phrasings for this tag, add them here so we can automatically correct them in the future. For example, suggest "bike" as a synonym for bicycle, or "sock" for socks.. equipment currently has no approved synonyms.. see all tag synonyms ». Users with more than 1250 reputation and a total answer score of 5 or more on the tag, can suggest tag synonyms. Users with a total answer score (total upvotes minus total downvotes) of 5 or more on the tag, can vote for tag synonyms. Suggestions will be automatically approved when they reach a score of 4, and automatically deleted when they reach a score of -2. ...
Incorrectly tagged questions are hard to find and answer. If you know of common, alternate spellings or phrasings for this tag, add them here so we can automatically correct them in the future. For example, suggest "bike" as a synonym for bicycle, or "sock" for socks.. pre-fermentation currently has no approved synonyms.. see all tag synonyms ». Users with more than 1250 reputation and a total answer score of 5 or more on the tag, can suggest tag synonyms. Users with a total answer score (total upvotes minus total downvotes) of 5 or more on the tag, can vote for tag synonyms. Suggestions will be automatically approved when they reach a score of 4, and automatically deleted when they reach a score of -2. ...
Je vous souhaite la bienvenue sur notre forum, en espérant quil vous plaira et que vous inscrivez pour nous faire partager votre folie, " Plus on est de fous, Plus on rit " ;D.
Je vous souhaite la bienvenue sur notre forum, en espérant quil vous plaira et que vous inscrivez pour nous faire partager votre folie, " Plus on est de fous, Plus on rit " ;D.
The work presented here evolved within the framework of a project that examines gene expression of neurological conditions in animal models. Using conventional methods (candidate genes study) gene expression analysis is limited. Hence, the aim was to establish a procedure like SAGE (serial analysis of gene expression) that allows for analysis of the entire transcriptome. As shown it is possible to perform SAGE in a standard laboratory. Minor changes to the original version were made. A special computer program was developed and evaluated to reduce sequencing errors. In addition to a description of the entire statistical process, the statistics of SAGE were explored by simulating normal SAGE experiments, using 4 statistical tests. One test version (modified Z-test) that has not been used for statistical analysis of SAGE yet was applied and reviewed. To assess the reliability of SAGE the total-RNA of 4 corteces of mice was extracted and combined. This basic transcript population was divided in two ...
Distribution of GO categories. The comparison of the distribution of unique transcripts (isotigs and singletons) between U. gibba and U. vulgaris transcriptomes
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