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how to extract protein info for a bunch of IDs

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

uniprot protein ncbi
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updated by Elisabeth Gasteiger Elisabeth Gasteiger • written by Learner Learner

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?

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written by st.ph.n st.ph.n

@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

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written by Learner Learner

if you have fasta file with multiple uniprot sequences:

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

input.fa is input fasta

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written by cpad0112 cpad0112

2 answers

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

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written by Eslam Samir Eslam Samir

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.

• 0 views • link
written by Elisabeth Gasteiger Elisabeth Gasteiger

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