The Basic Local Alignment Search Tool is a widely-used tool for finding and evaluating DNA or protein sequences. Users can utilize either their own sequences or the genomes of hundreds of organisms. It can be found at http://blast.ncbi.nlm.nih.gov/Blast.cgi

learn more… | top users | synonyms

3
votes
1answer
17 views

why does the score matrix influence the E value (BLAST)

When I align two HBB protein sequences wich have 80% identity, I used two kind of score matrices: Blosum62 and PAM30, to figure out the impact on my results. I noticed that the bit score is higher ...
0
votes
0answers
27 views

Determine OTU identity using Blastn full database or organism specific database?

I am seeking opinions on the best way to determine OTU identity using Blastn. Would the best way to identify an OTU be to blast the OTU to the full nr/nt Nucleotide collection or to blast your OTU to ...
1
vote
2answers
40 views

How is e-value calculated in BLAST 2 sequences (BLAST+)?

In the BLAST+ packages, you can align two sequences instead of searching a database: tblastn -query seq1.fa -subject seq1.fa The web BLAST documentation states ...
3
votes
1answer
55 views

Why are sequencing reads shorter than PCR products?

I have desinged and tested primers for RT-PCR, then purified the PCR products from the gels and send them to sequence at GATC (SUPREMERUN) using the forward primers. After blasting the reads to ...
0
votes
1answer
71 views

BLAST(Basic Local Alignment Search Tool) is heuristic?

How can we say that BLAST is based on a heuristic algorithm, as after finding one common word in the query sequence and a database sequence it performs pairwise alignment by dynamic programming - ...
4
votes
2answers
187 views

Basic Local Alignment Search Tool (BLAST)

Why would BLASTP (Basic Local Alignment Search Tool) be a poor tool to search for motifs in protein sequences?
1
vote
1answer
61 views

Do the BLAST scores have any relation between them?

Is there any relation among the BLAST scores (E-value, similarity, identity, gap, bit score)? Is the e-value score for an alignment proportional to other scores, such as similarity score (i.e. the ...
1
vote
1answer
45 views

How to Determine the Most Conserved Sequence from BLAST Result?

I used BLAST to find the best aligned DNA sequence to my query sequence. The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I ...
3
votes
1answer
51 views

blastn: What substitution matrix is used?

I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length. For amino acids I am able to use the substitution matrices in Biopython ...
2
votes
2answers
89 views

How to remove duplicate results from BLAST?

If I run BLAST using a protein sequence (e.g. human p53), I get many matches to the same protein, presumably from different research projects. As you can see from the screenshot, all are similarly ...
1
vote
1answer
71 views

Primer Design with Primer-BLAST over specific site

I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site. I am looking at KRAS for which I believe the RefSeq ID is NG_007524.1 and the forward ...
0
votes
0answers
66 views

Determining the percentage of the query of an alignment from a BLAST output

Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that ...
1
vote
2answers
100 views

Primer Design With Primer-BLAST

I am trying to design primers for sanger sequencing snp detection. In the past I have used Primer-BLAST, but I'm trying to pick up KRAS codon 12 mutations. The problem is that in Primer-BLAST you ...
3
votes
0answers
160 views

How to get only perfect matches with blastn? [closed]

I have installed Blast locally and I've configured the nucleotide database to use. I want to search some sequences (from a .fastafile) in this genome. So I used blastn: ...
1
vote
2answers
91 views

Aligning multiple sequences in heterogeneous group

I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have seq1, seq2.... seq10, ...
2
votes
1answer
217 views

what the best E-value cutoff in the miRNA homology search

I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop ...
6
votes
1answer
347 views

Find protein homologs with BLASTp

I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases. I'm using evalue of 0.00001 as threshold. I would like to filter queries having hits with >90% ...
2
votes
2answers
164 views

Local BLAST Copy Number per Hit

I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at ...
1
vote
1answer
41 views

programmatic fast search of 100-1000 short reads to a public server and obtain list of nearby genes

What are the options for programmatic fast searching of 100-1000 short reads to a public server and obtain list of nearby genes where the reads map? Input: ~100-1000 short reads Output: GFF list of ...
1
vote
1answer
71 views

BLASTn vs ORF tools

Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. This means that sometimes the genomic sequence that you download from a database ...
1
vote
1answer
32 views

Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an ...
4
votes
1answer
514 views

The parameter for setting the number of mismatches in standalone blast

In a standalone blast search, is there a parameter that could be specified to fix the number of mismatches allowed in an alignment. I went through the parameters and I could only find parameters to ...
2
votes
2answers
321 views

Primer design and BLAST E value stringency

When searching for misprimings I have been told that an e value that is higher than 0.01 is ok and will produce no significant amounts of mispriming. Yet I searched some and it would seem that the e ...
1
vote
2answers
228 views

How do you find pre-miRNAs from mature miRNA Blast output?

So in short, I did a blastn with standalone blast using all known miRNAs against the EST sequences in a genome (word length 7 and e-value 0.01). Now to confirm one of the next steps would be obtain ...
4
votes
2answers
212 views

GO terms for non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have ...
4
votes
4answers
439 views

Is there a PSI-BLAST for nucleotide sequences?

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs ...
1
vote
2answers
438 views

Blast a sequence against multiple databases

I would like to BLASTP a list of protein sequences in fasta format against multiple protein databases. Since I'm only interested in the first hit of each database, it is possible that BLAST result ...
0
votes
1answer
23 views

How to get conservation of vaccine candidates between hundreds of bacterial strains?

We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about 200). I would ...
3
votes
3answers
613 views

Bioinformatics tool for “pairwise alignment” of complementary sequences?

I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate ...