Questions tagged [blastp]
The variant of BLAST (Basic Local Alignment Search Tool) used for protein sequence alignment.
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How to BLAST a protein against a large set of organisms?
I have a list of organisms with their full scientific names and Taxonomy IDs, total ~1500. I want to BLAST my protein against this 1500 genome or proteome. How can I do that?
Here a sample protein ...
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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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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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Mismatch between mutant gene and reference gene outside the site of mutation
I am tasked with designing primers for a particular mutant (Target Gene Locus: At1g28490 i.e. SYP61) of Arabidopsis, obtained from Gabi-Kat:
The NCBI reference sequence for the genome goes:
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How are BLAST record scores calculated in biopython
Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
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Number of collinear genes are zero while running MCScanX
I am trying to do a synteny analysis using MCScanX. As per requirement I have done all by all blast between two sets of protein from two closely related species. And also prepared the gff file. The ...
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makeblastdb creating multiple files of unexpectedly large sizes
I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version ...
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blastp option to compare with a personal database
I'm trying to compare proteins generated with prokka (from a genome) with blastp using a virulence factor database VFDB, and I want to use some parameters obtained from this paper:
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FASTA and PDB: How to specify chain?
For proteins that have multiple chains (e.g., 1EMS), is there an easy way to specify which chain I want to use for blastp?
I cannot imagine that I am the first person to have this problem, but so far ...
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Blastp MSA to the same length
To generate aligned protein sequence truncate to the same length, I use blastp in biopython for MSA. I have multiple queries and one subject sequence. However, the alignment never returns the same ...
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How to do BLASTP for short sequences (<20 aa) effectively?
I am trying to find sequence homology between viral sequences and my protein of interest. I have the sequences of their epitopes which varies from 5 to 500 amino acids long. For shorter sequences, it ...
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should I continue the iteration of psiblast if the blast step produced only below threshold sequences?
I used a PSIBLAST (position specific scoring) to detect the similarities between specific proteins and the database of Clostridium.
The results did not reveal any similarities above the e value ...
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How to filter blast results from blast run against virulence factor database
I downloaded virulence factor database from here , to predict virulence genes from few genomes that my lab sequenced. I performed local blast on the database with default setting and found around ...
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How to export web NCBI tBLASTn results in table format with many queries?
Context
I'm an MSc student working on writing up my thesis (back home now) from my laptop and, therefore, unfortunately don't have access to a workstation/server capable of doing the tBLASTn search ...
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How to determine a protein's cellular location based on its sequence?
I am wondering about the appropriate workflow to determine a protein's cellular location based on its sequence.
Let's say I have a sequence like this from a fasta file
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