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*  Contig mapping | definition of Contig mapping by Medical dictionary
Looking for online definition of Contig mapping in the Medical Dictionary? Contig mapping explanation free. What is Contig mapping? Meaning of Contig mapping medical term. What does Contig mapping mean?
http://medical-dictionary.thefreedictionary.com/Contig+mapping
*  Publication - The Elizabeth H. and James S. McDonnell III Genome Institute at Washington University
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to ...
http://genome.wustl.edu/publications/detail/integrated-and-sequence-ordered-bac-and-yac-based-physical-maps-for-the-rat-genome/
*  OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly | BMC Systems Biology | Full Text
On the E. coli data, OMACC and FINISH made two and nine mis-connections, among which the true contig paths did not exist in the contig graph in two and seven cases, respectively. Detailed investigations reveal three major reasons for the absence of the true contig paths. First, some true contig paths are not continuous on the genome. For example, the true contig path between "85+" and "48+" is "85+:116+:112-:18-:52+:95-:51+:11-:53+:125+:80+:111+:48+" (Table S1, Additional file 1). Along this path, all the neighboring contigs connect without gaps (,2 bp) except "52+" and "95-", in-between which a gap of 166 bp exists. It is likely that this gap region is not sequenced at all. As a result, the two contigs "52+" and "95-" are not connected in the contig graph. Strictly speaking, the path should not be called a true contig path because there should be a ...
https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-S6-S7
*  DNA sequence & contig assembly software|Sequence assembly, analysis and mutation detection software
Tired of manual DNA sequence assembly? DNA Sequence Assembler: automatic DNA sequence assembly, analysis, editing & mutation detection
http://www.dnabaser.com
*  Sequence assembly software for multilocus sequence typing
STARS is an alternative interface to staden for sequence assembly for sequence typing projects. Sequence typing projects typically involve the sequencing of the same gene, or gene fragment, many times in order to determine polymorphisms. The standard staden interfaces, pregap4 and gap4,are more suited to assembling long contigs. The STARS interface, on the other hand has been designed with sequence typing projects in mind and allows the assembly of large numbers of short contigs into the same database. These contigs can be retrieved and edited from the interface using a standard staden contig editor. The system also performs user logging etc and can therefore be used as a lab database for your projects. The software was initially designed for managing sequencing projects using Multi Locus Sequence Typing (MLST) of bacteria. It is available free of charge under the General Public License. This software is for UNIX systems and you will first ...
https://pubmlst.org/software/assembly/
*  Bio::Assembly::Contig - search.cpan.org
Bio::Assembly::Contig stores much information about a contig in a Bio::Assembly::SeqFeature::Collection object. Relevant information on the alignment is accessed by selecting features based on their primary tags (e.g. all features which have a primary tag of the form '_aligned_coord:$seqID', where $seqID is an aligned sequence ID, are coordinates for sequences in the contig alignment) and, by using methods from Bio::Assembly::SeqFeature::Collection, it's possible to select features by overlap with other features.. We suggest that you use the primary tags of features as identifiers for feature classes. By convention, features with primary tags starting with a '_' are generated by modules that populate the contig data structure and return the contig object, maybe as part of an assembly object, e.g. drivers from the Bio::Assembly::IO set.. Features in the features collection may be associated with particular aligned sequences. ...
http://search.cpan.org/dist/BioPerl/Bio/Assembly/Contig.pm
*  Maize FPC Map
Publications Wei, F., E. Coe, W. Nelson, A.K. Bharti, F. Engler, E. Butler, H. Kim, J.L. Goicoechea, M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M. McMullen, G. Davis, J.E. Bowers, A.H. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund, and R.A. Wing (2007). Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3:e123. Nelson, W, A Bharti, E Butler, F Wei, G Fuks, H Kim, R Wing, J Messing, and C Soderlund (2005). Whole-Genome Validation of High-Information-Content Fingerprinting. Plant Physiology 139:27-38. Gardiner J, Schroeder S, Polacco ML, Sanchez-Villeda H, Fang Z, Morgante M, Landewe T, Fengler K, Useche F, Hanafey M, Tingey S, Chou H, Wing R, Soderlund C, Coe EH. (2004) Anchoring 9,3971 maize expressed sequence tagged unigenes to the bacte rial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiology 134:1317-1326. Coe E, Cone K, McMullen M, Chen S, Davis ...
http://www.agcol.arizona.edu/fpc/maize/
*  The Genome Factory: What bacterial genome assemblers are people using?
in-house software v. 10/18/2012 Unknown program v. before 2013-07-02 Direct Sequencing DNASTAR SeqMan NGen v. 4.0.0 GS Reference Mapper v. September 2013 Trimmomatic v. 0.32; Ion Torrent PGM Artimis v. 10.1 artimist v. 10.1 De Bruijn graph v. Apr-2011 BCFtools Consensus BLASTN v. actual BOWTIE v. Version 2.1.0 BWA v. 0.5.1 BioNumerics v. 6.6 ELAND alignment algorithm Galaxy v. May 2012 de Bruijn graphs v. Mar-2013 MAQ v. 0.7.1 MATLAB v. R2013a ...
http://thegenomefactory.blogspot.com/2016/04/what-bacterial-genome-assemblers-are.html
*  DNA sequence assembler|DNA sequence alignment/assembly/analysis, contig editing, SNP mutation detection & chromatogram viewer...
Affordable ($69) software for automated DNA sequence assembly, contig assembly, mutation detection, chromatogram editor. Sequence assembly, assemble DNA chromatograms, find heterozygous point mutations, automatic end clip
http://www.dnabaser.com/download/DNA-Baser-sequence-assembler/index.html
*  Living in an Ivory Basement - streaming elk
We obtained 377,980,276 raw reads (i.e., 300 bp sequences from random points in the genome), containing a total of 113.394 Gbp of sequence, or approximately 40X coverage of the tule elk genome. More than 98% of these data passed quality filtering. The reads (and coverage) were distributed approximately equally among the 4 elk, resulting in approximately 10X coverage for each of the 4 elk.. .... The tule elk reads were de novo assembled into 602,862 contiguous sequences ('contigs') averaging 3,973 bp in length (N50 = 6,885 bp, maximum contig length = 72,391 bp), for a total genome sequence size of 2.395 billion bp (Gbp). All scaffolds and raw reads will be made publicly available on Genbank or a similar public database pending publication. Alignment of all elk reads back to these contigs revealed 3,571,069 polymorphic sites (0.15% of sites). Assuming a similar ratio of heterozygous (in individuals) to polymorphic (among the 4 elk) sites as we ...
http://ivory.idyll.org/blog/tag/streaming-elk.html
*  Endotoxin-tolerant Mice Have Mutations in Toll-like Receptor 4 (Tlr4) | JEM
Using high-resolution genetic mapping techniques, we have restricted the position of the Lps gene to a 0.9-cM region of chromosome 4, flanked proximally by D4Nds9 and distally by D4Mit178. A 1.7-Mb cloned DNA contig spanning this interval was sequentially assembled using YAC, BAC, and P1 clones. Our data differ significantly from another recently published physical map encompassing the Lps locus ((37)). In this contig, a gap (estimated at 100 kb by fluorescence in situ hybridization) exists in the BAC contig between D4Nds9 and D4Mit178. Comparison of BAC clone addresses common to both maps suggests that this gap corresponds to the center of our contig, and is ∼950 kb in size. Finally, through cDNA selection and nucleotide sequencing of randomly cloned sheared BACs from our contig, we have identified three transcription units within the Lps candidate region, including Tlr4, and two novel genes.. We provide ...
http://jem.rupress.org/content/189/4/615
*  Assembler Tasm Software Downloads
Assembler Tasm. Download32 is source for assembler tasm shareware, freeware download - Advanced Assembler , PopAsm, the Popular Assembler , asmx , MiniDV Assembler 0.96 , Flat Assembler for Linux, etc.
http://www.download32.com/assembler-tasm-software.html
*  CerealsDB
schema_version": 0.1, "provider": { "name": "CerealsDB", "description": "A service to give information about SNP markers; e.g., the sequence upon which they are based, obtain primers used for their identification, identify the haplotypes of common UK varieties.", "url": "http://www.cerealsdb.uk.net/cerealgenomics/cgi-bin/parse_json_v3.cgi" }, "services": { "path": "Contig service", "summary": "A service to obtain contig information", "description": "A service to obtain contig information using SNP names, contig names or generic search terms", "operations": [ { "operationId": "Contigservice", "summary": "An operation to obtain contig information using SNP or Contig names", "description": "An operation to obtain contig information using SNP or Contig names", "parameter_set": { "parameters": [ { "param": "SNP_id", "name": "SNP id", "default": "BS00003643", ...
http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/web_API.php
*  DNA BASER Assembler - affordable sequence assembly - Download
DNA BASER Assembler - affordable sequence assembly, free and safe download. DNA BASER Assembler - affordable sequence assembly latest version: Tool used to assemble DNA samples.
https://dna-baser-assembler-affordable-sequence-assembly.en.softonic.com/
*  VGA v1 - Viral Genome Assembler
VGA v1 :: DESCRIPTION VGA is a method for accurate assembly of a heterogeneous viral population consisting of individuals viral genomes (also known as quasi-species). ::DEVELOPER ZarLab :: SCREENSHOTS N/A :: REQ
http://www.mybiosoftware.com/vga-v1-viral-genome-assembler.html
*  eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria | BMC...
The eRP arrangement strategy enable large-scale contig arrangement that allows for an observation of the genomic structure using the replication behavior that is common to all living things without requiring sequence information. The base composition bias, skewed oligomers, and gene directions are representative of biological information that is related to the genomic structure. However, in the case of de novo genome sequencing, there are not many cases in which the gene direction or replication origin and terminus are clearly annotated. This strategy overcomes these limitations by employing replication behavior in the genome assembly.. The use of biological information in genome assembly or scaffolding has become more common since the introduction of GFinisher, a tool that use the base compositional bias called GC skew [34]. In this study, we utilized the intracellular replication behavior as new biological information. Our research revealed that the replication behavior could clearly be ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4162-z
*  virus's written in assembler?
Since I am incredibly stupid when it comes to computers, i thought assembler was a programming language like C or C++ and could run on any machine. Only recently did I discover that the Assembler language changes by which computer you are using it, so that it is much harder for comptuers to trade programs and source code with each other. This brings me to virus's, which I have read to be sometimes written in assembler. My question is, how does a program written in a particular version of a
http://www.antionline.com/showthread.php?254272-virus-s-written-in-assembler&p=734509&viewfull=1
*  Distribution of contigs by size of longest ORF. Solid l | Open-i
Distribution of contigs by size of longest ORF. Solid line, contigs with any database homology by BLASTX (1,445). Dotted line, contigs without database homology
https://openi.nlm.nih.gov/detailedresult.php?img=PMC154577_gb-2003-4-4-r26-4&req=4
*  Design of 454 pyrosequencing contig generated from the | Open-i
Design of 454 pyrosequencing contig generated from the digestion of genomic DNA with restriction enzymes (EcoRI and BspEI), the addition of restriction site spe
https://openi.nlm.nih.gov/detailedresult.php?img=PMC2874759_1471-2156-11-32-2&req=4
*  High-Resolution Whole Genome BAC Rearrays - Human, Mouse, Rat
This file presents validation information showing the degree of corroboration of clone mappings in the fingerprint map and sequence. For each clone in the rearray, a 10-clone neighbourhood is selected from neighbouring canonical map clones with sequence coordinates. The union of sequence coordinates of these map clones from a set of neighbourhoods against which the clone's sequence position is compared.. The last field in this file reports the level of corroboration: "inside" indicates that the clone's sequence mapping is within its map-derived neighbourhood, "outside" indicates that the clone's position is on a different chromosome than suggested by its map-derived neighbourhood, "NUM" when the field is a number the clone is on the same chromosome as the neighbourhood, but not overlapping, and the number is the distance between the two positions, "none" indicates that the clone had no coordinate-bearing neighbours.. ...
http://mkweb.bcgsc.ca/bacarray/?view=download_mouse
*  Preparation of a 3-kb Mate-Pair Library for Illumina Sequencing
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
http://molecularcloning.com/index.php?prt=123
*  Omics! Omics!: Complete Genomics Goes Long
Ultimately, there is a relatively small limit on the size of a fragment (generally well under a kilobase, though I think I've seen discussion on SEQAnswers of kilobase+ fragments in Illumina) which can function in the systems, so to go longer mate-pair approaches were developed. These generate two reads known to be separated by a relatively long distance, on the scale of kilobases. These solve the problem by a bunch of trickery eliminating the intervening DNA but retaining linked tags. Such schemes typically involve shearing, ligation (or in vitro recombination) into circles, another shearing step, capture of the junction fragments and conversion into a library. A bunch of work, and with a number of serious disadvantages. In particular, they tend to require tremendous amounts of upfront DNA, often tens of micrograms. The length of the original inserts are limited by what can be efficiently circularized. Most mate pair approaches shoot for under 20Kb, though Lucigen has a clever kit aimed to ...
https://omicsomics.blogspot.com/2012/07/complete-genomics-goes-long.html
*  FPC V9.4 Release
MTP default behavior has been adjusted to permit MTP calculation from BES alignments to reference pseudomolecules or other long sequences (as opposed to short draft contigs from low-coverage sequencing). Previous behavior can be recovered by setting the Multiple Contig Ratio parameter to 3 (on the MTP Advanced Settings dialog). Default track behavior was changed so that all track types show by default, even if empty, unless removed by the user through the contig window track functions. This fixes a bug in which newly created projects did not show any tracks. ...
http://www.agcol.arizona.edu/software/fpc/r94.html
*  ABySS 1.0.12 - Canada's Michael Smith Genome Sciences Centre
Both ABYSS and KAligner are run only once per assembly, which speeds up the paired-end assembly stage by nearly a factor of two. The k-mer coverage information is correct in every contig file. A tool is included to convert colour-space contigs to nucleotide contigs. Discard reads that fail the chastity filter.
http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.0.12/
*  51-2023.00 - Electromechanical Equipment Assemblers
Perceptual Speed - The ability to quickly and accurately compare similarities and differences among sets of letters, numbers, objects, pictures, or patterns. The things to be compared may be presented at the same time or one after the other. This ability also includes comparing a presented object with a remembered object. ...
https://www.onetonline.org/link/details/51-2023.00