Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Removing redundant sequences
0
gravatar for kutubjoy
2.1 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 • 1.2k views
ADD COMMENT • link •
modified 5 months ago by Eslam Samir • 90 • written 2.1 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 2.1 years ago by Ram ♦ 12k
0
gravatar for nterhoeven
2.1 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 2.1 years ago by nterhoeven • 80
0
gravatar for h.mon
2.1 years ago by
h.mon ♦ 7.5k
Brazil
h.mon ♦ 7.5k wrote:

As Ram suggested, there are several tools to do this, one is cd-hit.
ADD COMMENT • link written 2.1 years ago by h.mon ♦ 7.5k

This is an old question :)

ADD REPLY • link written 2.1 years ago by Ram ♦ 12k
1

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

ADD REPLY • link written 2.1 years ago by h.mon ♦ 7.5k
0
gravatar for Kurban
8 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 8 months ago by Kurban • 160
0
gravatar for Eslam Samir
5 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 5 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 5 months ago by Ram ♦ 12k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1515 users visited in the last hour