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Old 07-19-2011, 06:08 AM   #1
papori
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Default blastx against UniProt

Is there any tool for doing alignment of local data against UniProt?

For example,
if i did an assembly for transcriptome , and i want to check the reliability of my contigs.
How can i align it against UniProt or other Database?

Thanks all
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Old 07-19-2011, 07:00 AM   #2
westerman
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I think you answered your own question: use blast. A local copy of blast can be made to align your sequences against any local database that you have created via the use of 'formatdb'. As an example using the older blast (instead of blast+)

'formatdb -i my_download_copy_of_uniprot -p T -n uniprot

Then

blastall -i my_local_sequences -d uniprot -p blastx -o out.blastx


If you want a web-based solution then going to the source (http://www.uniprot.org/) will allow blasting.
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Old 07-19-2011, 07:09 AM   #3
papori
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hi westerman,
Did you mean that i have to download all the database?
great idea!
thanks
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Old 07-19-2011, 07:24 AM   #4
papori
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Which of these is recommended for blast?
UniProtKB/Swiss-Pro or UniRef100/90/50

thanks
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Old 07-19-2011, 07:32 AM   #5
westerman
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Quote:
Originally Posted by papori View Post
Which of these is recommended for blast?
UniProtKB/Swiss-Pro or UniRef100/90/50

thanks
Well, it depends on what you are looking for. Thus you should be the one to decide after the descriptions of both. If I was to choose one for you I would go for UniRef because that will give you curated data without giving you false positives that you will need to chase down.
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Old 12-26-2012, 06:50 PM   #6
bioinfotlc
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Hi, you may try following sequence alignment web tool without installation/setup . Select Query Type - Nucleotide-Protein and search against database "SwissProt Protein UPKB"

a. SynaBlast - single query submission - http://synasite.mgrc.com.my/synasuit...enu.jsp?modN=1
b. SynaBlastMega - multiple query submission - http://synasite.mgrc.com.my/apps/syn..._BlastMega.jsp
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