I have a vast collection of peptide sequences from a proteomics analysis and I would like to match them to the corresponding exons. Does anyone know a user friendly tool/software to do this in a fast and reliable way?
I did a quick search and I found a this article:
Article Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes
Does anyone have experience with the PoGo software?
Would you recommend it? Or you think there are better alternatives for non-experts in bioinformatics?
Hi Anchel
the easiest way for you would be to use the BLAT tool from the UCSC website (http://genome-euro.ucsc.edu/cgi-bin/hgBlat?hgsid=231362751_cQ0BC8I6tARkRae8Gr8NAUaFbpZa&command=start).
you'll just need to be sure to choose the right species and genome and query type as protein.
fred
Hello Frederic and Chen,
Thank you for your suggestions!
I should clarify that I don't need to identify the peptides, I know the corresponding genes. What Im looking for, is an easy tool to find out the specific exon from which each peptide is coming. Of course, this is very easy to do when you have few peptides, but I have sequences from thousands of different proteins.
I agree with Frederic that, so far, the best option seems to be BLAT, because it's the only one (as far as I know) that allows you to submit multiple sequences at once (25 each time). However, this is still very slow to explore thousands of sequences, and you still need a second step of searching the genome to find each exon (one by one) because the output is genome locations.
So, as you see, I would like to find a high-throughput and one-step way of doing this.
Im trying to test PoGo (https://www.sanger.ac.uk/science/tools/pogo), the software I suggested, but it's not really user-friendly nor stand-alone. I need some more time to learn how to use it and figure out whether it's really useful for my purpose or not. In the meantime, more suggestions are welcome!
Hi Anchel,
I see, it's very specific and the best way would be to instal the UCSC database and tools (one mirror in fact) on your computer (http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads) to avoid being limited with the 25 entries option of BLAT. you can also download the BLAT alone (see BLAT in the Utilities paragraph).
fred
Hi,
Mapping tool (PoGo) can be used to quickly and efficiently identify genomic loci of peptides and post-translational modifications. Using reference gene annotation and an associated transcript translations PoGo identifies the genomic loci of peptides given as input and generates output in different formats borrowed from genomics and transcriptomics which can be loaded in various genome browsers such as UCSC Genome Browser, Ensembl Genome Browser, BioDalliance, and the Integrative Genomics.
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