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Questions tagged [blastp]

The variant of BLAST (Basic Local Alignment Search Tool) used for protein sequence alignment.

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2 votes
1 answer
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How to blast UniProt/RefSeq database from local clusters?

I want to identify all members of several protein families and study the evolutionary relationships between them. I tried to do exhaustive search for proteins homologous to a sequence via blast (...
antbirdINFINITY's user avatar
2 votes
3 answers
77 views

Comparing sequence similarity of two sets of peptide sequences?

What tools can we use to compare two sets of peptide sequences? The biological question is I have some kmer sequences of some proteins and would like to know how similar are these kmer sequences ...
Johnny Tam's user avatar
2 votes
2 answers
82 views

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 ...
Supertech's user avatar
  • 606
2 votes
2 answers
215 views

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 ...
con's user avatar
  • 125
1 vote
1 answer
55 views

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 ...
Jacob's user avatar
  • 11
0 votes
1 answer
69 views

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: ...
AvadaMouse's user avatar
3 votes
1 answer
55 views

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 ...
Tim Kirkwood's user avatar
1 vote
1 answer
239 views

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 ...
Kishor Kumar Sarker's user avatar
1 vote
1 answer
407 views

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 ...
accibio's user avatar
  • 145
1 vote
1 answer
110 views

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: ...
abraham's user avatar
  • 115
0 votes
2 answers
751 views

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 ...
lazer-guided-lazerbeam's user avatar
2 votes
2 answers
237 views

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 ...
Simon's user avatar
  • 195
1 vote
1 answer
1k views

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 ...
Riq's user avatar
  • 35
1 vote
0 answers
142 views

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 ...
ADHD's user avatar
  • 19
3 votes
1 answer
421 views

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 ...
Ahmed Abdullah's user avatar
4 votes
1 answer
77 views

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 ...
user3883's user avatar
6 votes
2 answers
342 views

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 ...
Cleb's user avatar
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