Tools for identifying/verifying protein (without accession number)

jenyl · 01-20-2015, 06:34 AM

If I have a series of protein sequences (experimentally obtained) that yield no results from BLAST, are there any other online/software tools that can be used to either identify or verify that these proteins exist?

GenoMax · 01-20-2015, 06:39 AM

If you obtained these sequences experimentally then they definitely exist

Have you tried psi-blast or better yet delta-blast @NCBI?

jenyl · 01-20-2015, 06:46 AM

They're not annotated in databases such as UniProt/Swiss-Prot so I'm not sure how I can "prove" that they are indeed real and transcribed from genes.

All I have are the protein sequences themselves though, won't I need accession numbers or ID to run them through psi/delta-blast?

GenoMax · 01-20-2015, 07:22 AM

You just need fasta sequence for doing delta- or psi-blast. You can limit your search against swissprot or refseq if you want well annotated proteins.

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01-20-2015, 06:34 AM	#1
jenyl Junior Member Location: uk Join Date: Jan 2015 Posts: 2	Tools for identifying/verifying protein (without accession number) If I have a series of protein sequences (experimentally obtained) that yield no results from BLAST, are there any other online/software tools that can be used to either identify or verify that these proteins exist?

01-20-2015, 06:39 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	If you obtained these sequences experimentally then they definitely exist Have you tried psi-blast or better yet delta-blast @NCBI?

01-20-2015, 06:46 AM	#3
jenyl Junior Member Location: uk Join Date: Jan 2015 Posts: 2	They're not annotated in databases such as UniProt/Swiss-Prot so I'm not sure how I can "prove" that they are indeed real and transcribed from genes. All I have are the protein sequences themselves though, won't I need accession numbers or ID to run them through psi/delta-blast?

01-20-2015, 07:22 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	You just need fasta sequence for doing delta- or psi-blast. You can limit your search against swissprot or refseq if you want well annotated proteins.