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Consider inclusion of CD-hit for selection of representative sequences out of large datasets (Read 2253 times)
Aug 30th, 2017 at 3:42pm

Peacemaker   Offline
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Thank you for the great improvements that ugene has seen over the last couple of years.
I would like to suggest to include the software cd-hit (http://cd-hit.org) as a plugin. This would help to reduce the complexity of large datasets of homologous sequences by automatically selecting representative sequences which feature identities below a certain identity threshold. I would suggest to consider including the two basic functions of the cd-hit suite, cd-hit for protein sequences and cd-hit-est for DNA sequences (http://weizhongli-lab.org/cdhit_suite/cgi-bin/index.cgi).
Thank you for your consideration.
 
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Reply #1 - Aug 30th, 2017 at 8:34pm

Yuliya Algaer   Offline
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Dear Peacemaker,

Thanks for your request!

We will add this feature in future UGENE versions.

However, this feature is quite big and it now has middle priority for us. If you need the feature to be implemented as soon as possible, you might consider to use our commercial support services.

Anyway, thank you again for the request! We will keep it in mind, while planning the UGENE future version.
 
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Reply #2 - Dec 28th, 2020 at 11:29pm

alfredlan   Offline
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Sir Peacemaker. Thanks for posting such a wonderful post. It is very helpful.
 
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Reply #3 - Jan 14th, 2021 at 10:27pm

jhonny   Offline
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Thanks for the peace maker.
 
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Reply #4 - Feb 3rd, 2021 at 10:50am

finnstan3   Offline
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Is there a way that you can include the feature on CD-hit for selection of representative sequences out of large datasets.  If it is not too much to ask.
 
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Reply #5 - Feb 17th, 2021 at 11:04pm

Kenny   Offline
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Thank you for this post.
 
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Reply #6 - Mar 25th, 2021 at 9:32pm

Brielle Luna   Offline
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This is definitely such a huge hit way back then. It is really impressive.

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