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Look for similar DNA sequences to a given sequence in the NCBI database

Hi everybody!

For a project, I'm trying to look for similar DNA sequences to a given sequence in the NCBI database, not necessarily from the same species, for example: given a DNA sequence found in a cat, I want to look for a similar one in different reptiles.

Thanks in advance.

ncbi dna
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updated by Ram Ram • written by erans995 • erans995

Thank you very much for your quick reply, but I need to do it in JAVA code. I couldn't find any way to run blast search in JAVA, any ideas?

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written by erans995 • erans995

I need to do it in JAVA code

yes, I'm sorry, that was clearly specified in your question....

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written by Pierre Lindenbaum Pierre Lindenbaum

in Java

Why Java specifically? Is this an assignment?

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written by Ram Ram

Yes, this is an assignment. If you have any other idea in another language, it's also okay. cpp preferably :>

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written by orelsmail • orelsmail

Are you and erans995 the same person?

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written by Ram Ram

We are partners to this assignment

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written by orelsmail • orelsmail

Pierre has given you the lead to the solution, try implementing it yourself and come back to us if you have specific questions.

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written by Ram Ram

Hey there. We've been looking all over the internet, and couldn't find a way to run a blast search in a java program. Also, we tried to access through the url, but there is no way to achieve the search results..

We are really frustrated and in need of help. All we really need is a program to run a blastn search in java.

Thanks ahead.

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written by orelsmail • orelsmail

You said CPP is OK too. Did you look for a way to run blast in CPP? It'd be a little difficult to believe that BLAST doesn't have APIs in two mainstream languages.

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written by Ram Ram

Found nothing, tried everywhere,that's why we're asking here. If there is something you guys know, please leave a link here.

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written by erans995 • erans995

It's a group assignment,we're partners. If you help him, you help me!

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written by erans995 • erans995

1 answer

use blastn https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome with 

Organism : Reptilia (taxid:8504)
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written by Pierre Lindenbaum Pierre Lindenbaum

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