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
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What protein or other process does the peptide BPC-157 come from?
BPC-157 is a peptide for which there were some studies that suggest that it can help with wound healing and gastrointestinal problems in some animal models. In 2022 the World Anti-Doping Agency added ...
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How to align more than 2 sequences with Needleman-Wunsch?
I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-...
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Slightly different sequences returned by BLASTP
Probably this is very trivial but I am self-learning bioinformatics and I don't know who to ask for this kind of stuff. Also, apparently it is really hard to find information on general topics like ...
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How to customize the output of my BLASTP output form
I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with ...
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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 ...
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How to identify an unknown species from its genome sequence [closed]
I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to ...
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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 ...
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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 ...
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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 ...
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blast search against UNIPROT
I would like to ask how i can search in blast against UNIPROT (TREMBL PLUS SWISSPROT) for a selected organism. In the BLAST site there is no option about UNIPROT(only Swissprot), and in the uniprot ...
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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 ...
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Is it PSI-BLAST or BLASTP if I use PSI-BLAST for only one iteration
In my case, I used PSI-BLAST in the local BLAST+ to search queries against the self created database. After the first search, I added the searched result to the database and then conducted the ...
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Why do the RNAseq reads map to only a certain region of a viral genome?
I am looking at RNAseq data and mapping them to 3 RNA segments from Cucumber Mosaic Virus.
I trimmed the adapters from the fastq files and converted them to fasta, which I searched against a virus ...
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Does diamond tblastn exist?
I actually want to use diamond instead of blast because it is faster with small sequences and big genomes, but I actually want to make a tblastn with several protein sequences as queries and the ...
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How to determine which is the nucleotide sequence of a gene?
I have came across a few genes that show different nucleotide sequence in different databases. I then found out that the sequences are actually reverse complement of each other. How do i determine ...
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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 ...
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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 ...
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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 "...
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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, ...
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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.
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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/...
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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 ...
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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 ...
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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. ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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?
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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 ...
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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 ...
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My BRIG run is suspiciously quick. What is a typical length of time for a run?
I use the BRIG (BLAST Ring Image Generator) program to compare prokaryote genomes. It executes a local BLAST+ and visualizes the results as rings around the reference genome. I downloaded three ...
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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 ...
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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 ...
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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 ...
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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 - ...
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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?
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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:
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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, ...
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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 ...
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