Can anyone please suggest me tool for fast alignment (input: eukaryotic gene sequences (769 KB) and database is NRDB)

Question

[Sudhir Jadhao]

Hi guys, Can anyone suggest me tool that is faster than blastx.

My input is : eukaryotic transcript (Average 769 KB) Database is :NRDB

There are lots of tool available online but those only work for small reads.

Or It will be good to use tools that are faster than blast but only develop for small reds ?

Thank you Inadvance

[Sudhir Jadhao]

Thank you guys for replay. I will try above suggestion and let you know

Answer 1

[GenoMax]

I assume you know about DIAMOND and Pauda. I am not sure if they will work with longer sequences.

What about good old blat if you are mainly interested in homologous sequences?

Answer 2

[Juke34]

Have a look at this publication. They tried many tools. It could help you in your choice. Unfortunately they didn't try neither diamond or Pauda (Was it existing at this time ? I doubt...)

Hiroaki Iwata and Osamu Gotoh Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res. 2012 Nov; 40(20): e161. doi:  10.1093/nar/gks708

Answer 3

[Biogeek]

Diamond or else RAPSEARCH2

Answer 4

[Prasad]

You can use usearch or vsearch tool. which are similar to blast but way faster than blast.

Answer 5

[Juke34]

If you are looking only at the fastest and you don't care about the splice aware alignment you could use NsimScan