Questions tagged [blast]
Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.
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Remote NCBI's Blast Perl API: maximising hits returned via command line
Question and Background I'm using NCBI's Blast Perl API to interrogate Genbank for example blastp. I don't get the throughput using their point and click web stuff.
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IgBLAST Error: Germline annotation database could not be found in [internal_data] directory
I'm in the following situation and I came here to see if I could get some help.
I'd like to use IgBLAST for an analysis on some Alpaca antibody data, so I received some FASTA sequences from a ...
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How to get full alignment output from BLASTP?
I am running a blastp search:
time ~/bin/ncbi-blast-2.14.0+-src/c++/ReleaseMT/bin/blastp -db nr -query X.fasta -out nr.X -num_descriptions 4000 -remote
but I have ...
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NCBI Blast databases - cannot find some databases
I'm working with a system that does local BLAST searches using some preconfigured BLAST databases. From what I see, these were updated within the last year, but I cannot find any current databases ...
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compare fasta sequences in pairs and collect metrics
I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline.
I would like to compare pair ...
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Extract specific nucleotide base position for query and subject from text file
I have an input file looks like this:
...
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Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?
Given a set of genes in a FASTA-formatted file, for example: exFasta.fa, what is the best way to determine how well conserved the genes in that file are among an ...
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Gene symbol list for all protein coding genes in mice
How can I get a csv or a list of the gene symbol names for all the protein coding genes in mice? I have RNA sequencing data and I'm not interested in the non-coding stuff. I'm worried it could mess ...
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Print indel/mismatch in a blastp stream
I am in need of a simple tool that accepts an XML file generated by a BlastP as input and gives me back a file containing information about mismatches/indels/etc. Fortunately such a tool already ...
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How can I identify the virulence factors in my FASTQ files generated from nanopore sequencing bacteria DNA?
I have performed genomic sequencing using nanopore technology and upon analysing using BLAST in the command line I have identified the presence of E.coli. I was wondering if I can add some code to ...
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What do you use the CLANS program for?
I am reading this paper called Birth and death in the Terminal Complement pathway, doi : https://doi.org/10.1101/2022.04.21.489004 where they have performed CLANS analysis.
I understand that CLANS ...
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What are all the proteins used to train Alphafold 2?
I want to identify the proteins used on AlphaFold2. The website says it was trained on PDB files from before April 30th 2018, and templates that are used are from no later than Feb 15 2021 (although ...
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Is there an equivalent of Entrez queries for local BLAST?
I have been having some trouble with running command line BLASTn remotely. Therefore, upon recommendations, and considering I have >100 searches planned, I am considering just downloading the nt ...
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Remote blastn - what is breaking my (bash) loop?
I am trying to search the NCBI non-redundant database for sequences similar to a few other (~40) sequences that I already have.
So I've tried running blastn remotely, and looping through multiple ...
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How to identify [hyper]thermophilic proteins by BLAST search?
I need to find homologs of certain proteins by BLAST search or similar. But I want filter (select) homologs from organisms that are classified as thermophilic or hyperthermophilic. I am wondering if ...
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tblastn not providing full alignment even on exact-matching sequences
I am using tblastn to search a polypeptide seq against transcripts. One of those transcripts contains the residues for that exact polypeptide once translated, yet BLAST only gets 88% of it rather ...
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Assign multiple taxids to a sequence when constructing a local BLAST database
I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two ...
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PSSM Matrix in PSI-BLAST
After running PSI-BLAST one obtains a profile matrix with this header:
A R N D C Q E G H I L K M F P S T W Y V
How does PSI-...
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How to retrieve fasta sequence after local blast?
I have created a Blast database using a reference genome. Then, I have performed a local blast search in command line using a gene of interest. I have obtained some hits with the usual Blasting ...
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Identifying Variant Conservation Across Species
I've got gene sequences of mouse genes. Each sequence contains variants from the reference genome. I need to find out whether these SNPs/variations are in functionally significant regions (i.e. exons)....
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blastn returning an inferior alignment
In my work I've found that in circumstances where there is a mismatch near the edges of the query sequence, blastn prefers to return a shorter contiguous alignment, rather than allowing for a mismatch ...
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How do you search for new enzymes that are more stable for handling, immobilization?
Noob here. I get that I should deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, ...
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mpiblast alternatives?
I am looking for a sequence alignment software capable of pairwise alignment of a large number of protein sequences (10^7).
I tried to go for mpiblast: https://wiki.canterbury.ac.nz/display/UCHPC/...
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How to use SRA Toolkit to blast SRA accessions?
I'm trying to look for a gene in a group of SRA files. Web BLAST can't cope with them, so I assume they're too large. I've tried tblastn_vdb from the SRA toolkit, as follows. It had previously worked ...
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Pseudocode for gapped BLAST seed extension
I am trying to understand in detail how does the gapped BLAST seed extension DP algorithm works. Despite searching for days now, I could not find anywhere a pseudocode that would allow implementing ...
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Timeout when downloading the ncbi nr blast database
I am experiencing timeout problems when downloading the NCBI nr preformatted blast database using the update_blastdb script (version 504861).
I run the script with the following paramters
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How low does an E-Value need to be for a gene to code for the same protein as query?
I'm looking at a bacterial genome and trying to find specific PEGs (Protein Encoding Genes) by BLAST searching. I'm taking the genes found with the lowest E-value in order to psiBLAST them to check it ...
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What kind of BLAST do I need to do to accomplish this task?
(I am a complete newbie to bioinformatics, so please bear with me!).
I recently used BLAST to compare a 500 bp nucleotide sequence in S. cerevisiae to a bunch of other 500 bp nucleotide sequences in ...
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Find species from FASTA files
In a school project we got the task of finding the species from two FASTA files. We got some hints of what to look for, like it is a unicellular eukaryote and that we can use blast. We don't know if ...
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How to identify genes from a genome assembly of C. Elegans?
I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
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How to read E-value annotation on NCBI BLAST?
I am seeking clarification on how to read the E value annotation on NCBI's BLAST results.
What I understand so far:
E -values are the expected value of the number ...
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What is the meaning of letter 'c' in tblastn results before genomic sequence position?
An example of a result. So far I have been unable to find the answer on my own.
">CP000000.0:c2005000-2006000 Escherichia coli strain XYZ chromosome
ATG..."
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Does BLASTClust guarantee that proteins in different clusters are dissimilar?
I need to find dissimilar proteins. Looking through the PDB I found the weekly BLASTClust results of proteins that are 30% similar. However, I do not know if protein A in cluster 1 is guaranteed to be ...
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Please help me with my command!
I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
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How to identify unknow bacterium species from whole genome genetic sequence
I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole.
I am currently using ILLUMINA PE data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled ...
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BLASTn query coverage discrepancy
Using the BLASTn webtool with,
Query Seq: CAATTGCGAAGCCACATTATT
Subject Seq: CP031332.1
BLASTn returns a single hit to CP031332.1 with query coverage at 100%.
However if one looks at the alignment, ...
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NCBI blast for exact match of a 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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Does NCBI's blast API block my IP?
I am trying to run a blatn command from both my laptop and within a google colab notebook. I am not sure why, but this command runs properly once and then, on the ...
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How to find possible viral subsequences in a Eukaryote genome?
I have an assembly of an algae and want to find if it has anything analogous to endogenous retroviruses' subsequences in its DNA.
My guess is I should manually blastn all subsequences until I find (or ...
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Software for taxonomic assignment?
I have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I already know to be reliable ...
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how to have a blast xml file in a readable and understandable way
I got a blast xml file after a DNA sequence search. The XML file is not very readable. What is the way to make it more understandable? This blast contains about twenty matches. Here is the xml file
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Do you know a program/script to count how many sequences have mismatches on each position of my primers?
I'm working with primer analysis and design, and so far I've performing it in Excel but: a) I don't like Excel, b) I do it manually, c) I don't like Excel, d) it gets tedious when working with ...
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Blast results filters
I performed a blastn search of NGS data against ssRNA database download from Internet, with a expected value 10-4. The size of NGS data reads is of 125 bp.
I have analyzed the blast results of the ...
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Standalone Blast+; Automating searches, Blastn formatting, interpretation
I am struggling with using NCBI's standalone blast, particularly the blastn feature.
I have a large number of nucleotide sequences that I want to use blastn to ID. The goal is to retrieve information ...
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Analyzing a blast result of NGS data
I am analyzing BLAST results from total RNA NGS, pair ends. This BLAST results was performed against the ssRNA virus database download from NCBI.
I filtered those read data whose paired ends ...
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Can you give me a detailed explanation about PrimeBlast?
I am trying to write a research paper on PRIMER-BLAST. I have read something about it on
https://www.ncbi.nlm.nih.gov/pubmed/22708584/
but still, it is not enough. So can you please tell me more ...
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how could i find uniprot ac in blast?
I have made a search in p-blast.
I would like to search for the protein results in uniprot. how can I do it directly?
I can go to GENBANK but i would like to go to UNIPROT.
Thank you!!!
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Primer-Blast Custom Database [error]
I'm using Primer-Blast to compare a PCR template against a custom database of reference sequences, using Primer-Blast's Custom database functionality.
However whenever I try to upload a FASTA file as ...
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how can i search in p-blast against UNIPROT(not only swissprot)
i need to search for one protein against UNIPROT in BLAST for a selected organism.
How can I do it? (SWSISSPROT+TREMBL)
THANKS!!
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phmm blast hmmer
i have created a phmm in hmmer from a multiple alignment focused on E. coli produced in tcoffee from sequences taken from blast similar to my query sequence.
I would like to ask how i can compare the ...
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