Searching Fasta File For Specific Ids

Question

[andysw90]

Hi all,

Apologies if this is answered elsewhere, I've searched for it but can't find!

I have a list of UniProt IDs (e.g., Q95T64 Q8INK6 Q9GNK5) and want to search through them all (n=~450) to see if they exist in a fasta file of a species, outputting two lists, one list of the IDs that do appear in the species fasta, and one list of those that do not!

Grep perhaps?

Many thanks

Andy

EDIT: The list of IDs are contained within a .txt file, return seperated

Answer 1

[Andrzej Zielezinski]

On linux just type:

sort <(cat list.txt) <(grep '>' uniprot.fa | cut -c5-10) | uniq -d

to get a list of UniProt IDs that are present in your fasta file.

If you want to list IDs that don't appear among fasta records, just change uniq -d to uniq -u.

[bulbul]

how shoulld i pull out the mutiple sequences from one fasta file by using gene id header in another text file?? what is command use in linux?

Answer 2

[Pierre Lindenbaum]

extract the IDs from the fasta header, sort both files, use comm

Answer 3

[KCC]

Python script below. Save it in a file like myscript.py

from sets import Set
import sys

# parameters: uniprotfile fastafile

uniprotfile = open(sys.argv[1])
fastafile = open(sys.argv[2])


A = Set([])

for line in uniprotfile:
    line = line.strip()
    A.add(line)

B = Set([])
for line in fastafile:
    if line.startswith('>'):
        line = line[1:].strip()
        B.add(line)


C = A.intersection(B) #names that are in both FASTA and UniProt list
print "Present:"
for el in C:
    print el

print
print "Not present:"
D = A.difference(B) #names not found in fasta
for el in D:
    print el

Next, run the script in this way: python myscript uniprot.txt fasta.fa