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searching for gene sequences, automated

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searching for gene sequences, automated

Postby poloke » Wed Jul 11, 2012 12:58 pm

Hallo all,

Recently I sequenced 3 pieces of DNA , now its pretty easy to check for similar genes in the ncbi databank: you just enter your sequence and you search... and you repeat this 3 times, since I had 3 genes.. However , what if someone has for example 300 genes to check?

Is their any option to automate this proces?
I am not an expert in bio-informatics and the use of the ncbi database, but I think it should be possible to automate this proces?
Eg: if someone sequences an entirely new genome, I can hardly imagine they manually enter each contig in the website and search for it...

Are their programs out there to automate this?
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Postby canalon » Thu Jul 12, 2012 1:22 am

Yes a lot.
If you look in the NCBI bookshelf they will explain you how to program that for yourself, and many if not most DNA analysis package do provide that option.
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Re: searching for gene sequences, automated

Postby poloke » Thu Jul 12, 2012 11:27 am

Do you have a specific link for it? I can go to the bookshelf, but those are just books, isnt there an online tutorial or something like that?
Or perhaps you know some programs that are easy to use?
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Postby canalon » Sat Jul 14, 2012 4:07 am

Geneious is great if you have a few thousand dollars that do not know how to use :(
I do not know of any free program doing that, but that is more likely a product of my ignorance.

As for what book in the bookshelf, I do not which one for sure, but it is likely one of those: http://www.ncbi.nlm.nih.gov/books?term=pubmed
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Re: searching for gene sequences, automated

Postby poloke » Sat Jul 14, 2012 11:53 am

As a student, I do not have thousands of dollars to spend :p
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Postby JackBean » Sun Jul 15, 2012 11:19 am

Even the BLAST _at_ NCBI web page gives you the opportunity to search with several sequences at once (I'm not aware what's the limit, maybe 20 or 200 sequences;)
http://www.biolib.cz/en/main/

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Re:

Postby poloke » Sat Aug 11, 2012 2:00 pm

JackBean wrote:Even the BLAST _at_ NCBI web page gives you the opportunity to search with several sequences at once (I'm not aware what's the limit, maybe 20 or 200 sequences;)


I seem to have overlooked this, where can you find this?
Can I simple add multiple sequences then? How do I seperate them when inserting multiple sequences?
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Postby JackBean » Sun Aug 12, 2012 12:36 pm

yes, just put them in in FASTA format:
>sequence 1 titel
SEQUENCE1SEQUENCE
STILLSEQUENCE1ETCETC
>sequence 2 ID
SEQUENCE2SEQUENCE AND THIS
CANGOONAND
ONANDONANDON:)
>sequence 3
ANDTHELASTONEBLAHBLAHBLAH


or inserting simply several NCBI IDs if you have them
http://www.biolib.cz/en/main/

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Postby triton » Wed Aug 22, 2012 7:40 pm

you can download ncbi database into your computer, install command line blast and do your search in you computer. You can have as many sequences as your processor tolerate. alternatively you can create an account in BIOPORTAL OSLO and use their cluster for blasting. You can submit milions of sequences in one file.
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