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urgi-anagen / TE_finder

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.
https://urgi.versailles.inra.fr/Tools/REPET
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Is it possible to use diamond or mmseqs as blast engine when running BLASTER? #1

Closed xiekunwhy closed 8 months ago

xiekunwhy commented 2 years ago

Hi,

As ncbi blast as well as WU-BLAST is too slow, would you please make some modification to accept diamond (https://github.com/bbuchfink/diamond) or mmseqs2 (https://github.com/soedinglab/MMseqs2) as blast engine?

Best, Kun

hquesneville commented 2 years ago

Dear Kun,

Thank you for this question and your interest in Blaster. Diamond and MMseq2 are well suited for protein search. I do not see really an added value to use Blaster in this context. For DNA search we tested Minimap2 which works well. It is quick but less sensitive as expected. I do not see today the added value to implement Minimap2 in Blaster, but perhaps you can explain me the usage you see ?

However keep in mind that blast is multithreaded and you can use it with several threads in Blaster by passing the correct parameter. By default Blaster run Blast with 1 thread.

Best regards,

Hadi

Hadi Quesneville Directeur de recherche / Research director Administrateur des Données Algorithmes et Codes de la recherche (ADAC) / Chief Data Officer

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Le 28 avr. 2022 à 20:18, xiekunwhy @.**@.>> a écrit :

Hi,

As ncbi blast as well as WU-BLAST is too slow, would you please make some modification to accept diamond (https://github.com/bbuchfink/diamond) or mmseqs2 (https://github.com/soedinglab/MMseqs2) as blast engine?

Best, Kun

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xiekunwhy commented 2 years ago

Dear Hadi,

MMseq2 can do DNA search, I am trying to prepare *.align file using mmseq2 results, and skip blaster step.

Best regards, Kun