how to extract protein info for a bunch of IDs

Question

[Learner]

I have many protein IDs, I want to know whether there is a way to extract only the first line of the Fasta file?

For example, for this protein Q02248

I want to extract the following

sp|Q02248|CTNB1_MOUSE Catenin beta-1 OS=Mus musculus GN=Ctnnb1 PE=1 SV=1

This is easy if I want to do for few, but when it comes to many, then it is hard

[st.ph.n]

Questions like this have been asked many times on Biostars. Have you searched for solutions?

This is easy if I want to do for few, but when it comes to many, then it is hard

What do you do for a few, that makes it easy?

[Learner]

@st.ph.n I did search and I could not find a solution. one by one i go to UniProt and get the Seq and download it. But if I want to do for many, it will be very time consuming. even if you have a solution to download with their sequence, It will be acceptable

[cpad0112]

if you have fasta file with multiple uniprot sequences:

seqkit seq <input.fa.gz>/<input.fa> -n

input.fa is input fasta

Answer 1

[Eslam Samir]

Here is my free program on Github SDDC (https://github.com/Eslam-Samir-Ragab/Sequence-database-curator)

It is a very fast program and it can deal with:

1. Nucleotide sequences
2. Protein sequences

It can work under Operating systems:

1. Windows
2. Mac
3. Linux

It also works for:

1. Fasta format
2. Fastq format

In your case use the filter mode. Here is all what you want to know about the program

Best Regards

Answer 2

[Elisabeth Gasteiger]

If your problem is obtaining the FASTA format for many UniProtKB identifiers at one, rather than downloading it one by one, you can use the batch retrieval service at http://www.uniprot.org/uploadlists

Please don't hesitate to contact the UniProt helpdesk in case of doubts. We try to monitor questions here but cannot always catch up.