Question: Removing redundant sequences
0
gravatar for kutubjoy
3.7 years ago by
kutubjoy0
United States
kutubjoy0 wrote:

I have a fasta file containing many protein sequences with identifier. How can I remove the redundant sequences using HMMscan

blast alignment sequence • 2.3k views
ADD COMMENTlink modified 2.0 years ago by Eslam Samir100 • written 3.7 years ago by kutubjoy0
1

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

ADD REPLYlink written 3.7 years ago by RamRS20k
0
gravatar for nterhoeven
3.6 years ago by
nterhoeven80
Germany
nterhoeven80 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 COMMENTlink written 3.6 years ago by nterhoeven80
0
gravatar for h.mon
3.6 years ago by
h.mon23k
Brazil
h.mon23k wrote:

As Ram suggested, there are several tools to do this, one is cd-hit.

ADD COMMENTlink written 3.6 years ago by h.mon23k

This is an old question :)

ADD REPLYlink written 3.6 years ago by RamRS20k
1

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

ADD REPLYlink written 3.6 years ago by h.mon23k
0
gravatar for Kurban
2.2 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 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 COMMENTlink written 2.2 years ago by Kurban170
0
gravatar for Eslam Samir
2.0 years ago by
Eslam Samir100
Germany / Würzburg / Universität Würzburg (IMIB)
Eslam Samir100 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 COMMENTlink written 2.0 years ago by Eslam Samir100
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 REPLYlink written 2.0 years ago by RamRS20k
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: 1370 users visited in the last hour