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Question: Removing redundant sequences
0
gravatar for kutubjoy
2.3 years ago by
kutubjoy • 0
United States
kutubjoy • 0 wrote:

I have a fasta file containing many protein sequences with identifier. How can I remove the redundant sequences using HMMscan
blast alignment sequence • 1.3k views
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modified 7 months ago by Eslam Samir • 90 • written 2.3 years ago by kutubjoy • 0
1

why use HMMscan to remove redundant sequences? There are a gazillion deduplication tools out there - just search the forum for FASTA deduplication.

ADD REPLY • link written 2.3 years ago by Ram ♦ 12k
0
gravatar for nterhoeven
2.2 years ago by
nterhoeven • 80
Germany
nterhoeven • 80 wrote:

I wrote a perl script to do that. It is called remove_duplicates and you can find it here:

https://github.com/nterhoeven/sequence_processing
ADD COMMENT • link written 2.2 years ago by nterhoeven • 80
0
gravatar for h.mon
2.2 years ago by
h.mon ♦ 8.6k
Brazil
h.mon ♦ 8.6k wrote:

As Ram suggested, there are several tools to do this, one is cd-hit.
ADD COMMENT • link written 2.2 years ago by h.mon ♦ 8.6k

This is an old question :)

ADD REPLY • link written 2.2 years ago by Ram ♦ 12k
1

Not for my standards, I even replied to 3-4 year old questions ;-)

ADD REPLY • link written 2.2 years ago by h.mon ♦ 8.6k
0
gravatar for Kurban
9 months ago by
Kurban • 160
Urumqi
Kurban • 160 wrote:

Hello guys. I have more than 70,000 protein sequences come from 65 animal species, most of them are TFs. So some of them might be homologous. I like to use CD-HIT to remove the them. But which similarity threshold should I use? Any suggestion?
ADD COMMENT • link written 9 months ago by Kurban • 160
0
gravatar for Eslam Samir
7 months ago by
Eslam Samir • 90
Egypt / Cairo / Microbiology & Immunology Department
Eslam Samir • 90 wrote:

Here is my free program on Github Sequence database curator (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

Best Regards
ADD COMMENT • link written 7 months ago by Eslam Samir • 90
1

I see that you've created a Tool type post for your tool. Please do not spam threads with ads for your tool.

ADD REPLY • link written 7 months ago by Ram ♦ 12k
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