Question

Website that provides fasta sequences from Gene ID

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7.9 years ago

ksi216 ▴ 80

I was wondering if there was a website or tool I can get fasta sequences from a bunch of Gene ids?

geneid blast • 3.0k views

ADD COMMENT • link updated 12 months ago by Ram 43k • written 7.9 years ago by ksi216 ▴ 80

score 1 · Answer 1 · 2016-05-12

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7.9 years ago

GenoMax 141k

Are the ID's from a single organism? If so you could use BioMart on the relevant genome page at Ensembl or Table Browser tool at UCSC (if the genome is available from either location).
Not a web site based solution: but if those are NCBI ID's (can be from many organisms) then you could use blastdbcmd tool from Blast+ suite and nt/nr blast indexes to retrieve fasta sequences.

ADD COMMENT • link 7.9 years ago by GenoMax 141k

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they are Gene Ids from the human CCDS file from NCBI , they will be from the same chromosome. Sorry I didn't specify. So in that case is BioMart my best option ?

ADD REPLY • link 7.9 years ago by ksi216 ▴ 80

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the reason I need the fasta sequences is to blast the corresponding sequences from the Gene Ids, if only we could run a blast using the GENE id

ADD REPLY • link 7.9 years ago by ksi216 ▴ 80

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Web Blast @NCBI will accept accession numbers/gi so you could use Uniprot ID converter to convert your gene ID's to those.

ADD REPLY • link 7.9 years ago by GenoMax 141k

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As I mentioned with my comment before, a lot of things get simplified in this thread to a point where it is just wrong, so I have to say something. Blast is not accepting accession numbers. Blast is an algorithm. There are different implementations of this algorithm on different websites and tools. But Blast does not accept anything. In your own interest, be more careful with the wording and meaning of terms - and also read a bit about the background of the methods instead of just 'using' it - it will help in the long run.

ADD REPLY • link 7.9 years ago by LLTommy ★ 1.2k

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Since the discussion was about websites Blast I was referring to was @NCBI. I have clarified my post above to include that information.

ADD REPLY • link 7.9 years ago by GenoMax 141k

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how do i do that ? is there a link on bioperl ?

ADD REPLY • link 7.9 years ago by ksi216 ▴ 80

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You can put CCDS IDs into Ensembl BLAST.

ADD REPLY • link 7.9 years ago by Emily 23k

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I think that genomax2 touched an important point here, and obviously what I was thinking right away - so ks216: What is a gene id? Where do you get your id's from? There is not a world wide unique id for everything. You have to ask yourself some more questions and understand the complexity of bioinformatics and its services.

ADD REPLY • link 7.9 years ago by LLTommy ★ 1.2k

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I am new to this, I was under the impression that the Gene Ids were unique, but that's not the case. I understand that blast is an algorithm. thank you all for your help.

ADD REPLY • link 7.9 years ago by ksi216 ▴ 80

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Hey, it is ok that you are new to this, don't get me wrong. All I try is to open your eyes a little bit. There are many many services and many many different databases . There often is not one solution, but many. Often it is not clear what the best solution is, rather you have to test some and find out yourself what works best for your experiment. This is truly a real challenge in bioinformatics and that is why I want to help you to understand this. So keep that in mind in the future.