Removing redundant sequences

Question: Removing redundant sequences

5.7 years ago by

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 • 3.6k views

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modified 4.0 years ago by Eslam Samir • 100 • written 5.7 years ago by kutubjoy • 0

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 5.7 years ago by Ram ♦ 32k

5.7 years ago by

nterhoeven • 120

nterhoeven • 120 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 5.7 years ago by nterhoeven • 120

5.7 years ago by

h.mon ♦ 32k

Brazil

h.mon ♦ 32k wrote:

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

ADD COMMENT • link written 5.7 years ago by h.mon ♦ 32k

This is an old question :)

ADD REPLY • link written 5.7 years ago by Ram ♦ 32k

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

ADD REPLY • link written 5.7 years ago by h.mon ♦ 32k

4.3 years ago by

Kurban • 190

china/Urumqi/xinjiang academy of animal scinces

Kurban • 190 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 4.3 years ago by Kurban • 190

4.0 years ago by

Eslam Samir • 100

Germany / Würzburg / Universität Würzburg (IMIB)

Eslam Samir • 100 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:

Nucleotide sequences
Protein sequences

It can work under Operating systems:

Windows
Mac
Linux

It also works for:

Fasta format
Fastq format

Best Regards

ADD COMMENT • link written 4.0 years ago by Eslam Samir • 100

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 4.0 years ago by Ram ♦ 32k

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