Protein blast sequence alignment. Medical search. Frequent questions

An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers. (myexperiment.org)
Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. (myexperiment.org)
A sequence similarity search often provides the first information about a new DNA or protein sequence. (nih.gov)
There are many ways of performing a sequence similarity search, but probably the most popular method is the "Basic Local Alignment Search Tool" ( BLAST ) ( 1 , 2 ). (nih.gov)

The bioinformatics tools include those for analyzing 2D-GEL patterns, protein modeling, and protein identification. (nhbs.com)

BLAST 2 Sequences' utilizes the BLAST algorithm for pairwise DNA-DNA or protein-protein sequence comparison. (nih.gov)
COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. (nih.gov)
Pairwise constraints are then incorporated into a progressive multiple alignment. (nih.gov)
Gap opening penalty and gap extension penalty for gaps inside of a sequence used in pairwise global alignment in the progressive alignment stage. (nih.gov)
Gap opening penalty and gap extension penalty for gaps at ends of a sequence used in pairwise global alignment in the progressive alignment stage. (nih.gov)
A straightforward comparison procedure using pairwise protein sequences similarities was suggested in Rankprot [26], in addition to distance-profile methods reported in [29]. (columbiagypsy.net)
By clustering together amino acids and reducing the alphabet that proteins are written in to fewer than twenty letters, we find that pairwise sequence alignments are actually more sensitive to proteins with similar structures. (caltech.edu)
Pairwise genome sequence alignment was conducted by using EMBOSS Needle software ( www.ebi.ac.uk/Tools/psa/emboss_needle/ ) with default parameters. (cdc.gov)

A search allows scientists to infer the function of a sequence from similar sequences. (nih.gov)
The megaBLAST nucleotide-nucleotide search, optimized for very similar sequences (in the same or in closely related species), first looks for an exact match of 28 bases, and then attempts to extend that initial match into a full alignment ( 3 , 4 ). (nih.gov)
Reduce computation time by using clusters of similar sequences. (nih.gov)
The idea behind using clusters is that constraints do not contribute information for alignment of very similar sequences. (nih.gov)
Clusters of similar sequences are found using alignment-free k-mer counting-based method. (nih.gov)
One useful way of discovering similar sequences is to align their sequences, as done e.g. by the popular BLAST program. (caltech.edu)

While the standard BLAST program is widely used to search for homologous sequences in nucleotide and protein databases, one often needs to compare only two sequences that are already known to be homologous, coming from related species or, e.g. different isolates of the same virus. (nih.gov)
The cross-reactions of MRP2/Mrp2 protein of different species with anti-human MRP2 polyclonal antibody were found by Western blotting. (aspetjournals.org)
However, because of the unknown binding affinity of antibody to MRP2/Mrp2 protein across species and lack of purified MRP2/Mrp2 proteins for calibration, the immunoblotting assay was excluded from the absolute quantification of MRP2/Mrp2 protein for multiple species. (aspetjournals.org)
By sequence similarity analysis and functional assays from the species Streptomyces lividans TK23, S. coelicolor A3(2) and S. glaucescens GLA.O, first hints for a widespread lack of MalP and presence of AmlE in the class Actinobacteria were given. (frontiersin.org)
The same domains may also occur in proteins from different species. (nih.gov)
Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for STB5 . (yeastrc.org)
To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. (biomedcentral.com)
Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine- F. circinatum interaction. (biomedcentral.com)
Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species. (biomedcentral.com)
Some extrinsic methods use genomic sequences from other species. (biomedcentral.com)
A cross-species comparison of genomic sequences can help in predicting genes in the given query sequence. (biomedcentral.com)
The amplified viral nucleic acid libraries of the bat species were then sequenced with the Illumina/Solexa GAII sequencer (Illumina, San Diego, CA, USA). (cdc.gov)

To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
The local alignment approach also means that an mRNA can be aligned with a piece of genomic DNA , as is frequently required in genome assembly and analysis. (nih.gov)
Finding protein-coding genes in eukaryotic genomic sequences with in-silico methods remains an important challenge in computational genomics, despite many years of intensive research work. (biomedcentral.com)
The first group consists of ab initio programs which use only the query genomic sequence as input. (biomedcentral.com)
The second group of gene-finding methods, extrinsic methods, comprises all programs which use data other than the query genomic sequence. (biomedcentral.com)
In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.com)
The located reads were then used for reads-based nested PCR to identify genomic sequences. (cdc.gov)

BLASTP performs protein-protein sequence comparison, and its algorithm is the basis of many other types of BLAST searches such as BLASTX and TBLASTN . (nih.gov)
PSI-BLAST first performs a BLASTP search to collect information that it then uses to produce a Position-Specific-Scoring-Matrix ( PSSM ). (nih.gov)
Which are some of the fastest protein-protein alignment algorithms, faster than blastp? (biostars.org)
quick comment: do NOT consider blastP as a protein aligner (or any kind of aligner for that manner). (biostars.org)

We report here the whole-genome sequences of the human-infective Trichuris trichiura and the mouse laboratory model Trichuris muris . (nature.com)
In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1. (researchsquare.com)
Advances in whole-genome sequencing technologies have enabled numerous key discoveries. (researchsquare.com)

BLASTX searches a nucleotide query against a protein database , translating the query on the fly. (nih.gov)
Those reads generated by the Illumina/Solexa GAII with length of 80 bases were directly aligned to the protein sequences in the National Center for Biotechnology Information nonredundant protein database by the blastx program in the BLAST software package, version 2.2.22 ( www.ncbi.nlm.nih.gov/blast ) with parameters "-e 1e-5 -F T -b 10 -v 10. (cdc.gov)

Nucleotide sequences were initially checked using the Basic Local Alignment Search Tool hosted by the National Center for Biotechnology Information ( http://blast.ncbi.nlm.nih.gov/Blast.cgim ) for comparison with other known nucleotide sequences. (who.int)

We conducted complete genome comparison and phylogenetic analysis on the basis of polymerase and spike protein. (cdc.gov)
The sequence contains a large open reading frame (ORF) encoding a polyprotein of 224.2 kDa with five domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase, and coat proteins), typical of marafiviruses. (bvsalud.org)
Noroviruses are associated with an compared to an established set of reference sequences to determine estimated 70,000-200,000 deaths annually [2,3 ] while sapoviruses genotypes and polymerase types based on phylogenetic clustering, or by primarily cause sporadic AGE in young children although outbreaks in employing NCBI BLAST web service. (cdc.gov)
In this paper, we describe the development and evaluation of an forces that drive norovirus evolution [ 9 , 10 ] and most frequently occur alternative web-based tool, Human Calicivirus Typing (HuCaT) tool for at the junction of the RdRp (polymerase) and VP1 (capsid) encoding typing of human norovirus and sapovirus sequences. (cdc.gov)
Polymerase chain reaction (PCR) was conducted using groEL PCR-restriction fragment length polymorphism and sequence analysis. (who.int)

We established the complete genome sequences of 2 betacoronaviruses (Bat Rp-coronavirus/Shaanxi2011 and Bat Cp-coronavirus/Yunnan2011), which are 29,484 nt and 29,452 nt, respectively. (cdc.gov)
In this work, we characterize the complete genome sequence of this virus, tentatively named purple passionfruit leaf deformation virus (PpLDV), and evaluate its distribution in Antioquia. (bvsalud.org)
in clone C6/36 cells, and its complete genome was sequenced. (bvsalud.org)

In practice DNA BLAT works well on primates, and protein BLAT on land vertebrates. (ucsc.edu)
In vertebrates this subfamily contains four proteins: TIF1α/TRIM24, TIF1β/TRIM28, TIF1γ/TRIM33, and TIF1δ/TRIM66, while only one protein, Bonus (Bon), is present in Drosophila , making it an attractive model to understand the conserved functions of TIF1 proteins. (elifesciences.org)
Telomeres are specialized structures at the end of chromosomes and consist of stretches of repetitive DNA (5'-TTAGGG-3' in vertebrates and trypanosomatids) and associated proteins [ 5 ]. (biomedcentral.com)

To deselect, click back on the nucleotide sequence. (addgene.org)
Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
List of restriction enzymes that can cut a given nucleotide sequence. (addgene.org)
List of common features detected in a given nucleotide sequence. (addgene.org)
List of commonly used primers detected in a given nucleotide sequence. (addgene.org)
A new virus, tentatively named "Pennisetum glaucum marafivirus" (PGMV), was detected, and its complete nucleotide sequence of 6364 nucleotides was determined. (bvsalud.org)
The nucleotide sequence of the complete PGMV genome shares 68.5% identity with that of sorghum bicolor marafivirus, and its coat protein shares 58.5% identity with that of oat blue dwarf virus. (bvsalud.org)
HuCaT uses an algorithm based on number of matching queries, k-mers are used to calculate the actual matching nucleic acid k-mers (short substrings of DNA [n 9 nt in number of nucleotide sequence matches for type assignment using the HuCaT]) to build alignments between query and reference sequences. (cdc.gov)

Here we present high-quality genome sequences for T. trichiura and T. muris , the first duo of a major human STH and its mouse counterpart. (nature.com)

If instead BLAST started out by attempting to align two sequences over their entire lengths (known as a global alignment), fewer similarities would be detected, especially with respect to domains and motifs. (nih.gov)
apart from the reason pointed out by jrj.healey , blast is designed (and optimized) to look for similarities between an input protein and a database of proteins based on (and this is where the confusion comes from) locally aligned similarities. (biostars.org)
ClustalW and bl2seq sequence analysis showed that LaTRF shared sequence identity with the Trypanosoma brucei TRF (TbTRF) protein and had the same degree of sequence similarities with the dimerization (TRFH) and the canonical DNA-binding Myb-like domains of both mammalian TRFs. (biomedcentral.com)

TBC1D30 is a gene in the human genome that encodes the protein of the same name. (wikipedia.org)
The gene for the protein includes two domains: the RabGAP-TBC domain, and the DUF4682 domain. (wikipedia.org)
The autosomal dominant monogenetic disease neurofibromatosis type 1 (NF1) affects approximately one in 3,000 individuals and is caused by mutations in the NF1 tumour suppressor gene, leading to dysfunction in the protein neurofibromin (Nf1) 1 , 2 . (nature.com)
in an operon with an upstream PurR/LacI-type transcriptional regulator gene, named amlR ( ACSP50_2475 ), and a gene downstream ( ACSP50_2473 ) encoding a GGDEF-EAL-domain-containing protein putatively involved in c-di-GMP signaling. (frontiersin.org)
In serotype 4b, gtcA appears to be the first member of a bicistronic operon which includes a gene with homology to Bacillus subtilis rpmE , encoding ribosomal protein L31. (asm.org)
In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. (biomedcentral.com)
Sensitive probabilistic modeling of extrinsic evidence such as sequence database matches can increase gene prediction accuracy. (biomedcentral.com)
Some of the best available ab initio gene prediction programs have been extended and have become more accurate by exploiting additional extrinsic data sources such as protein or EST sequences [ 13 ]. (biomedcentral.com)
have analyzed the tef-1α sequences of F. equiseti , as well as the toxin-related genes PKS13 , PKS4, and TRI5 [26], and Kari has successfully cloned a protease gene [27]. (researchsquare.com)
7 Primers designed to amplify the partial groEL gene encoding heat-shock protein of Anaplasma phagocytophilum EphplgroELF (5′-ATGGTATGCAGTTTGATCGC-3′) and EphplgroELR (5′-TCTACTCTGTCTTTGCGTTC-3′) were used and expected to yield a 625-bp product for Anaplasma phagocytophilum and for Anaplasma platys , respectively. (who.int)

Updating is required to keep using the tools that run Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE, as these will soon stop working in older versions. (ucsf.edu)
Clustal Omega gives some of the most accurate protein alignments to my knowledge, even if its a little slower, so it depends what you're trying to do/show. (biostars.org)

We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)
Students will be introduced to biological sequence data (DNA and protein sequences, whole genomes, learn to access major sequence databases and use a variety of web-based services. (uit.no)

Within L. monocytogenes , sequences homologous to gtcA were found in all serogroup 4 isolates but not in strains of any other serotypes. (asm.org)
In this work, we identified and characterized a Leishmania protein (LaTRF) homologous to both mammalian TRF1 and TRF2. (biomedcentral.com)

Quantification involves measuring the abundance or concentration of proteins, which can be done using various methods such as label-based or label-free quantification techniques. (proprofs.com)

Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
Direct DNA sequencing was performed using the same PCR primers. (who.int)
If the sequence result was of low quality, the amplicon was cloned into a plasmid vector using a TOPO TA cloning kit (Invitrogen, Carlsbad, California) and then sequenced using the primers provided with the kit. (who.int)

The BLASTN nucleotide-nucleotide search looks for more distant sequences. (nih.gov)

However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
Proteomics is the study of proteins and their functions within an organism. (proprofs.com)

Algorithms for estimating similarity between two macromolecular sequences are of profound importance for molecular biology. (iospress.com)

The availability of next-generation sequencing technology has circumvented this barrier for non-model organisms by enabling transcriptome assembly from high-throughput RNA sequencing (RNA-seq) data [ 9 , 10 ]. (biomedcentral.com)
On the basis of high-throughput transcriptomics data, we identify whipworm proteins that are highly expressed in the anterior region of the parasite, that is, in intimate contact with the cytoplasm of host intestinal cells and the immune system. (nature.com)
High-throughput sequencing (HTS) surveys of viruses in purple passion fruit fields in the province of Antioquia suggested infection by a new member of the family Tymoviridae. (bvsalud.org)

Perform a ClustalW multiple sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). (myexperiment.org)

The size column shows the number of amino acids in each protein isoform. (wikipedia.org)
BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. (ucsc.edu)
proteins, like DNA, are linear polymers written in a twenty-letter "language" of amino acids. (caltech.edu)

The total limit for multiple sequence submissions is 50,000 bases or 25,000 letters. (ucsc.edu)
Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. (myexperiment.org)
It is a local aligner, but that is very different from doing, for example, a multiple sequence alignment (even if the MSA does local alignment). (biostars.org)
COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information. (nih.gov)
Ranges of input sequences that match to the same conserved domain will be aligned to each other in the final multiple alignment. (nih.gov)
Pair wise locally aligned ranges of input sequences will be aligned to one another in the multiple alignment. (nih.gov)
Smaller values result in more clusters and hence more conserved domain-based constraints used in multiple alignment. (nih.gov)
Larger values result in fewer clusters and hence less conserved domain information used in multiple alignment. (nih.gov)
Multiple alignment editor. (linuxlinks.com)
Multiple sequence alignment using MUSCLE 3, KAlign, Clustal. (linuxlinks.com)

Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). (myexperiment.org)

In August 2018, a survey was conducted in the main producing regions of Burkina Faso, and leaf samples were analyzed using virion-associated nucleic acid (VANA)-based metagenomic approach and Illumina sequencing. (bvsalud.org)

The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. (researchsquare.com)

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. (addgene.org)
CSE 427: Computational Biology Algorithmic and analytic techniques underlying analysis of large-scale biological data sets such as DNA, RNA, and protein sequences or structures, expression and proteomic profiling. (washington.edu)
Living systems present us with beautiful and intricate structures, from the helices and sheets of a folded protein to the dynamic morphology of cellular organelles and the self-organization of proteins in a biomembrane and a synergy of theoretical and it in silico approaches should enable us to build and refine models of in vivo biological data. (caltech.edu)

The importance of telomeric proteins for telomere maintenance has increased our interest in the identification of homologues within the genus Leishmania . (biomedcentral.com)
LaTRF was predicted to be an 82.5 kDa protein, indicating that it is double the size of the trypanosome TRF homologues. (biomedcentral.com)

Among plants, particularly gymnosperms, genome size and complexity hindered sequencing and assembly of a reference genome. (biomedcentral.com)

UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. (ucsf.edu)
Despite the astronomical number of possible proteins sequences, a great amount of similarity is observed among the folded structures of globular proteins. (caltech.edu)

The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. (elifesciences.org)
We resolve chromosomal sequences and infer sex chromosome-specific parasite genes and new potential drug targets. (nature.com)

Only DNA sequences of 25,000 or fewer bases and protein or translated sequence of 10000 or fewer letters will be processed. (ucsc.edu)

Protein secondary structure prediction using GOR IV and PSIPRED. (linuxlinks.com)

We estimated the approximate locations of those reads on the CoV genome and their relative distances on the basis of alignment results exported with MEGAN 4-MetaGenome Analyzer ( http://ab.inf.uni-tuebingen.de/software/megan/ ). (cdc.gov)

High resolution two-dimensional electrophoresis of proteins. (pdbwiki.org)
A technique has been developed for the separation of proteins by two-dimensional polyacrylamide gel electrophoresis. (pdbwiki.org)
Separation involves techniques such as gel electrophoresis or liquid chromatography to separate proteins based on their size, charge, or other properties. (proprofs.com)

The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. (launchpad.net)
E-value threshold for accepting BLAST-P hits in pair wise local alignment of input sequences. (nih.gov)

Other non-telomeric proteins, such as the DNA repair proteins Mre11 and Rad51, also play important roles at telomeres [ 7 , 8 ]. (biomedcentral.com)

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. (ucsc.edu)
It will find perfect sequence matches of 20 bases. (ucsc.edu)

It is also possible to compare a protein or nucleotide query to a database of PSSM's. (launchpad.net)
TBLASTN searches a protein query against a nucleotide database , translating the database on the fly. (nih.gov)
PSI-BLAST can then search a database of protein sequences with this PSSM. (nih.gov)
RPSBLAST (Reverse-Position-Specific BLAST ) can very quickly search a protein query against a database of PSSMs that were usually produced by PSI-BLAST . (nih.gov)
DELTA- BLAST produces a PSSM with a fast RPSBLAST search of the query , followed by searching this PSSM against a database of protein sequences ( 5 ). (nih.gov)
In the setup phase, BLAST reads in the query , search parameters, and database . (nih.gov)
They are used to initiate matches in the database (or "subject") sequences. (nih.gov)
In the preliminary search, a number of steps are performed on every sequence in the database. (nih.gov)
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. (pdbwiki.org)
In this study, we focus on hints derived from matches to an EST or protein database, but our approach can be used to include arbitrary user-defined hints. (biomedcentral.com)
Other extrinsic methods use a database of known expressed sequences or proteins. (biomedcentral.com)

EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula . (biomedcentral.com)
Sequence similarity-based taxonomic assignments were conducted as described ( 7 ). (cdc.gov)

In-cluster sequences will be aligned using combined local and global alignment. (nih.gov)

Paste in a query sequence to find its location in the the genome. (ucsc.edu)
matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. (launchpad.net)
The query sequence to use is the input, the other parameters for the search are allowed to default. (myexperiment.org)
It may first check the query for low-complexity or other repeats, and then produces a set of "words"--short, fixed-length sequences based on the query. (nih.gov)
Query sequences to be aligned should be pasted in the text area. (nih.gov)
Use RPS-BLAST to find conserved domains in query sequences to guide alignment. (nih.gov)
COBALT is optimized for cases where groups of sequences do match to the same domain (see Query Clustering below). (nih.gov)
Unchecking this box will reduce computation time but will also result in poorer alignment (especially if Use query clusters box is checked). (nih.gov)
HMMGene, has an extension that integrates into the HMM information from BLAST alignments of the query sequence with cDNA, EST and protein sequences [ 15 ]. (biomedcentral.com)
Web-based to query sequences using a k-mer (DNA substring) based algorithm. (cdc.gov)
Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. (cdc.gov)

Conclusions The SVM-Freescore technique is been shown to be a good sequence-based analysis device for useful and structural characterization of conotoxin protein. (columbiagypsy.net)
Proteomics is a field of study that involves the identification and characterization of proteins. (proprofs.com)

Evaluates designs using sequencing, fluorescence assays, enzyme activity assays, and single cell studies using time-lapse microscopy. (washington.edu)

The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default. (myexperiment.org)
Click on the buttons below to submit a BLAST search to NCBI. (addgene.org)
Perform a BLAST search a. (myexperiment.org)
It is useful to break the BLAST search down into a few different phases called setup, preliminary search, and traceback . (nih.gov)
Blast is a search tool (aka sequence-google), not an alignment tool! (biostars.org)
The SCOOP approach [30] regarded as common sequence matches between two Pfam HMM profile search results, and performed better than elaborated methods such as HHsearch in detecting protein superfamily relationship. (columbiagypsy.net)

The TBC1D30 protein has been found in or associated with the cytoplasm and the plasma membrane from antibody studies. (wikipedia.org)

Use with SnapGene software or the free Viewer to visualize additional data and align other sequences. (addgene.org)
During the course, the students will learn to retrieve, analyze, compare and visualize genetic sequences. (uit.no)

Project of recently sequenced conotoxin in to the suitable superfamily utilizing a computational strategy could offer an efficient way of obtaining or adding precious preliminary information over the natural and pharmacological functions of these toxins. (columbiagypsy.net)

Table lists enzyme name and the sequence location of the cut. (addgene.org)

Moreover, a significant loss of Mrp2 protein in the membrane fraction of rat cryopreserved hepatocytes was observed. (aspetjournals.org)
Analysis of Membrane Proteins by Two-Dimensional Gels - Michael Fountoulakis, 15. (nhbs.com)
In the third and final case study we examine the forces between proteins in a lipid bilayer membrane. (caltech.edu)
Due to the bending of the membrane surrounding them, such proteins feel mutually attractive forces which can help them to self-organize and act in concert. (caltech.edu)
These finding are relevant at the areal densities estimated for membrane proteins such as the MscL mechanosensitive channel. (caltech.edu)
The findings of the analytical studies were confirmed by a Monte Carlo Markov Chain simulation using the fully two-dimensional potentials between two model proteins in a membrane. (caltech.edu)

Plasmid sequence and annotations. (addgene.org)
Use text editor or plasmid mapping software to view sequence. (addgene.org)
Thank you for your patience as we work to enhance our plasmid and sequence displays. (addgene.org)
To select a portion of sequence, click one location on the plasmid and then a second location to display the sequence between the two locations. (addgene.org)

It may miss more divergent or shorter sequence alignments. (ucsc.edu)
The BLAST algorithm is tuned to find these domains or shorter stretches of sequence similarity. (nih.gov)

Anatomy6

Organisms13

Diseases9

Chemicals and Drugs36

Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Psychiatry and Psychology1

Phenomena and Processes78

Disciplines and Occupations3

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Information Science40

Health Care16

Similarity search4

Bioinformatics1

Pairwise8

Similar sequences6

Species12

Genomic7

Blastp4

Whole-genome3

BLASTX2

Ncbi.nlm.nih.gov1

Polymerase5

Complete genome3

Vertebrates3

Nucleotide sequence8

Genome sequences1

Similarities3

Gene10

Clustal Omega2

Genomes2

Homologous2

Quantification1

Primers3

BLASTN1

Organism2

Algorithms1

High-throughput3

ClustalW1

Amino acids3

Multiple10

Phylogenetic tree1

Illumina1

Repetitive sequence1

Biological3

Homologues2

Reference genome1

Structures2

Genes2

Fewer1

Prediction1

Analyzer1

Electrophoresis3

Local alignment2

Play important roles1

Bases2

Database11

Taxonomic2

Global alignment1

Query11

Characterization2

Assays1

Search6

Antibody1

Visualize2

Computational1

Enzyme1

Membrane6

Plasmid4

Shorter2