Question: Non-Redundant Data Sets Of Protein
0
gravatar for eka0700
4.8 years ago by
eka070030
Bangladesh
eka070030 wrote:

Hello everyone,

I'm working with plant proteome. As there are huge number of proteins in a proteome, I want to filter out the protein number within a limited length of amino acids. Is there any tool available for this? And anyone for calculating the average length of amino acid sequences in plant proteomes?

Thanks in advance.

• 1.3k views
ADD COMMENTlink modified 4.8 years ago by richard.rymer10 • written 4.8 years ago by eka070030

What file type you're working with? Is it fasta?

ADD REPLYlink written 4.8 years ago by PoGibas4.7k

Yes, it is fasta.

ADD REPLYlink written 4.8 years ago by eka070030

What have you done already? Searching "filter fasta by length" on google got me several answers: How to Filter Multi fasta by length?? ; filter sequence by length ; How to Filter the Sequence by Their Length.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by PoGibas4.7k

Thanks. I've tried those. But it didn't work :(

ADD REPLYlink written 4.8 years ago by eka070030
1
gravatar for richard.rymer
4.8 years ago by
richard.rymer10 wrote:

Jalview can do this fairly easily, though if you use an entire genome's worth of proteins it may run very slowly. Just sort by length through calculate, and then you can highlight the range of sequences you want to remove, and just hit delete. Then save the "alignment" as a new fasta file.

ADD COMMENTlink written 4.8 years ago by richard.rymer10

Is multiple sequence alignment required before using Jalview?

ADD REPLYlink written 4.8 years ago by eka070030
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 840 users visited in the last hour