Question: Look for similar DNA sequences to a given sequence in the NCBI database
0
gravatar for erans995
5 months ago by
erans9950
erans9950 wrote:

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.

dna tool similar ncbi • 279 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by erans9950

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?

ADD REPLYlink written 5 months ago by erans9950
1

I need to do it in JAVA code

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

ADD REPLYlink modified 5 months ago • written 5 months ago by Pierre Lindenbaum113k

Have any idea though?

ADD REPLYlink written 5 months ago by orelsmail0

in Java

Why Java specifically? Is this an assignment?

ADD REPLYlink written 5 months ago by RamRS18k

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

ADD REPLYlink written 5 months ago by orelsmail0
1

Are you and erans995 the same person?

ADD REPLYlink written 5 months ago by RamRS18k

We are partners to this assignment

ADD REPLYlink written 5 months ago by orelsmail0
1

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

ADD REPLYlink written 5 months ago by RamRS18k

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.

ADD REPLYlink written 5 months ago by orelsmail0

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.

ADD REPLYlink written 5 months ago by RamRS18k

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

ADD REPLYlink written 5 months ago by erans9950
1

REST API and C++ toolkit discovered after literally 5 minutes of Google: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo ¯\_(ツ)_/¯



image

ADD REPLYlink modified 5 months ago • written 5 months ago by RamRS18k

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

ADD REPLYlink modified 5 months ago • written 5 months ago by erans9950
2
gravatar for Pierre Lindenbaum
5 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum113k wrote:

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

Organism : Reptilia (taxid:8504)
ADD COMMENTlink written 5 months ago by Pierre Lindenbaum113k
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