Questions tagged [blast]

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

Filter by
Sorted by
Tagged with
21
votes
4answers
2k views

Alternatives to NCBI BLAST during US government shutdowns?

Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences. However, during the last American government shutdown in 2013, ...
17
votes
1answer
3k views

Why would a 2019-nCoV protein sequence in the NCBI database match a protein submitted in 2018?

There seems to be a bit of a conspiracy theory brewing over some data in the NCBI database, and I don't have the necessary knowledge to make sense of it. It basically goes like this: Go to NCBI ...
14
votes
2answers
911 views

When does BLAST fail to align 2 DNA sequences?

This is an assignment that had confused me for a long time. So I think you guys who study computational biology might be interested. The original question is: Find the two most similar DNA ...
7
votes
2answers
6k views

Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

The Wikipedia page on BLAST states that: The scores are created by comparing the word in the list in step 2* with all the 3-letter words. By using the scoring matrix (substitution matrix) to score ...
6
votes
1answer
8k views

What is the meaning of "E-value" in the BLAST search?

After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that? https://en.wikipedia.org/wiki/BLAST This expectation or expect value "E" (often ...
6
votes
1answer
1k 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% ...
4
votes
3answers
995 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 (...
4
votes
1answer
2k 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 ...
4
votes
2answers
787 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 ...
3
votes
2answers
545 views

What direction is a sequence in databases written?

In many databases, the DNA sequences for proteins are given as a string of a,t,g,c without specifying whether the starting is from 5' or from 3'. Also it is not specified if it is the coding or non ...
3
votes
3answers
1k 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 ...
3
votes
1answer
3k views

Why does BLAST reduce word size for short proteins?

I'm using BLAST to identify a short protein (BLASTp). If I check the short query then the word size reduces from 3 to 2. However the search will then be less ...
3
votes
2answers
367 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?
3
votes
1answer
192 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 ...
3
votes
1answer
571 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 ...
3
votes
2answers
969 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 e-values,...
3
votes
1answer
46 views

Using BLAST for molecular replacement in structural biology

This is my first time trying to do molecular replacement to solve a protein structure. I am using the NCBI blastp program to find suitable search models. When choosing a search model, I understand ...
3
votes
0answers
1k 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: ...
2
votes
2answers
937 views

What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)

Both HMMER and BLAST report an e value for alignments. Is it calculated in the same way and - assuming that default settings are used - can they be compared directly (are the equivalent)? If not ...
2
votes
2answers
1k 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 ...
2
votes
2answers
75 views

How to selectively filter BLAST results for an endogenous retroviral LTR to retrieve members of the same ERV family?

I'm running a local BLAST search on a HERV-K(HML2) LTR sequence in the human genome. I get thousands of hits. I want to retrieve the hits that correspond to other HERV-K(HML2) LTR sequences only. ...
2
votes
1answer
560 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 ...
2
votes
2answers
959 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 ...
2
votes
3answers
402 views

BLAST with minimum E-value cutoff

It's easy to set the maximum E-value threshold in a BLAST request. I need to set the minimum E-value. Does anybody have any suggestions?
2
votes
1answer
94 views

How to restrict a BLAST search to include only a few protein sequences?

I am performing a BLAST search and I need to filter the output to a certain family of proteins. Specifically, I need to get matches within the CYP152 family of the Cytochrome P450 proteins. I can ...
2
votes
1answer
672 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 ...
1
vote
2answers
1k 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 ...
1
vote
1answer
97 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
39 views

Can conventional PCR amplify DNA from different organisms from a specimen in a single step?

I've understood so far that in conventional PCR, the most abundant DNA/genotype present in the speciment at the beginning of the reaction is selected and esponentially amplified. So that cPCR are ...
1
vote
1answer
273 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 ...
1
vote
2answers
335 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 ...
1
vote
1answer
167 views

How do I download entire human genome for local blast formatting and searching?

I'm trying to make a copy of the entire human genome for local blast queries on my machine. I understand that I need to download it from the NCBI FTP server here... ftp://ftp.ncbi.nih.gov/genomes/...
1
vote
1answer
103 views

How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?

I have a list of 100+ proteins and I need to conduct psi-blast for each one of them against "bacterial proteins" only. I went to NCBI's protein blast tool, but couldn't figure out how to select/limit ...
1
vote
1answer
139 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 ...
1
vote
2answers
166 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, ...
1
vote
1answer
47 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
2answers
335 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 ...
1
vote
1answer
58 views

BLAST, using Smith-Waterman in the last step and S-score

In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a ...
1
vote
1answer
80 views

Why are the results of local BLAST and miRbase BLAST different?

I am trying to reproduce locally on my computer what I get running mirbase on their website using BLAST. The search sequences is: mature miRNAs which I had downloaded on my computer and make it as a ...
1
vote
2answers
161 views

Blast databases

I am helping a colleague setup a local blast server. My background is computer science so I apologize if I use incorrect terminology. Using the NCBI blastn webpage, one of the databases listed is "...
1
vote
1answer
441 views

Lactobacillus casei and paracasei

I am carrying out a study of lactobacilli isolated from different samples. Genus and species are identified using a sequenced 1000pb long 16S fragment in BLASTn. I cannot distinguish between L. casei ...
1
vote
1answer
310 views

Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?

I have a data set of de novo assembled RNA-seq datasets across different sample types. When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. ...
1
vote
1answer
123 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
50 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 ...
1
vote
2answers
810 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 ...
1
vote
0answers
38 views

NCBI blast for exact match of short sequence

I'm trying to Blast for exact matches to the sequence: 'ATTGNNNNGCAAACCA' in the human transcriptome using NCBI Blast on its 'refseq_rna' database. However, when I do a basic query I get "No ...
1
vote
0answers
36 views

Understand and reproduce withdrawn publication method - Blastp - covid19

I try to reproduce the method of this withdrawn paper. I know this paper has been debunked and withdrawn. I am curious to understand the details of the method used on it. I am a programmer and I don't ...
1
vote
0answers
38 views

Creating BLAST database with nucleotide "place holder"

I have a set of nucleotide sequences that contain some special characters with multiple meanings: H -> C, A or T K -> G or T M -> C or A R -> G or A S -> C or G W -> A or T Y -> c or T I would like ...
1
vote
0answers
13 views

BLAST protein sequences from 2 different bacterial species

I am interested in finding a consensus sequence of a protein found in e.coli, in Pseudomonas aeruginosa. I am using pseudomonas.com to BLAST p the amino acid sequence of the protein that i have found ...
1
vote
0answers
44 views

Merge NCBI and Ensembl data

Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species. Let's say I have ...