Entering edit mode
8.6 years ago
ksi216
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80
I was wondering if there was a website or tool I can get fasta sequences from a bunch of Gene ids?
1
Entering edit mode
8.6 years ago
GenoMax
147k
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.
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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 ?
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
Web Blast @NCBI will accept accession numbers/gi so you could use Uniprot ID converter to convert your gene ID's to those.
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.
Since the discussion was about websites Blast I was referring to was @NCBI. I have clarified my post above to include that information.
how do i do that ? is there a link on bioperl ?
You can put CCDS IDs into Ensembl BLAST.
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.
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.
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.
how do i use the blastdbcmd from bioperl i didnt see a tutorial