orthology enrichment

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3.4 years ago

isha.lily20 ▴ 10

Hello Researchers,

1. Can any one tell me how to do a reciprocal blast?
2a . How do I identify conserved orthologous genes and annotation of specific sequences? and then
2b . How do I map specific sequences on conserved orthologous genes?

I tried taking 3 protein sequences of different species and did normal protein blast with specific e value 1*10^(-6) but I don't know what is reciprocal blast. How do I find evolutionary conserved orthologous genes?

Thank you

orthology • 1.1k views

ADD COMMENT • link updated 3 months ago by Ram 44k • written 3.4 years ago by isha.lily20 ▴ 10

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If a Reciprocal Best Hit (RBH) search is what you want to do, try the easy-rbh module from MMseqs2.

As for your second (and maybe third) questions, dig around in this book perhaps?

ADD REPLY • link 3.4 years ago by Dunois ★ 2.8k

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Please stick to one question
Tell us what you've tried on your own.

ADD REPLY • link 3.4 years ago by Ram 44k

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Hi Ram, I tried the same as mentioned exported 3 protein sequences of different species just did normal protein blast

ADD REPLY • link updated 3 months ago by Ram 44k • written 3.4 years ago by isha.lily20 ▴ 10

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Please google "reciprocal blast" - there are Biostars posts that address the topic. Always search online and try implementing a reliable solution you find on an online forum/paper.

ADD REPLY • link 3.4 years ago by Ram 44k

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