Question

Non-Redundant Data Sets Of Protein

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10.7 years ago

eka0700 ▴ 30

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.

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ADD COMMENT • link updated 10.7 years ago by richard.rymer ▴ 10 • written 10.7 years ago by eka0700 ▴ 30

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

ADD REPLY • link 10.7 years ago by PoGibas 5.1k

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Yes, it is fasta.

ADD REPLY • link 10.7 years ago by eka0700 ▴ 30

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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 REPLY • link 10.7 years ago by PoGibas 5.1k

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

ADD REPLY • link 10.7 years ago by eka0700 ▴ 30

score 1 · Answer 1 · 2014-03-11

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10.7 years ago

richard.rymer ▴ 10

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.