Re: [galaxy-user] Question from UCSC about SNPs and proteins
Hi Jen, "Mutate Codons with SNPs" tool under "Evolution" section on Galaxy should help to answer this question. If you look at the tool's help section, it explains the required format of the input dataset. The input should have start, end, stop and strand co-ordinates for each of the codons, joined with start, end, stop, strand co-ordinates and observed SNPs for each of the SNPs. If the user has these data in two separate files, he can join them using "Join" tool under "Operate on genomic intervals" section. The output of the tool will consist of codons in the input mutated with the respective SNPs. To check if the changes are synonymous or not, the user can join this output with a tabular file containing the genetic code using "Join two queries" tool under "Join, subtract and group" section. I hope this answers your questions. Please feel free to email us if you have any further queries. Also, please send any future Galaxy-related questions to our mailing list at galaxy-user@bx.psu.edu. Thanks! Guru Galaxy team. On Jan 29, 2010, at 7:54 PM, Jennifer Jackson wrote:
Hi Guru,
We have a question that we do not have a straightforward answer to. After reviewing the tools at Galaxy, I don't see a clear path to the answer, and was hoping you could help. Either to confirm there is no tool or to suggest a dataflow.
This is the thread so far, so you know where we are: https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021146.html https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021147.html https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021148.html https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021149.html
The short, the user has a list of novel SNPs and wants to know the change to the protein (perhaps also novel based off genomic). We have a web-mRna translation tool, but the user would then need to do the rest on his own: cut out the coding region, swap in the SNPs, translate via web tool, then analyze against a protein matrix for synonymous or non-syn changes. Protein only so far (although where they are taking it next - structural or functional implications, etc. we don't know - that is beyond the scope of the analysis we support, so far).
Is there a Galaxy tool or workflow that you could suggest? If yes, should I forward the question on to the galaxy help list? Would that be the right place to send it? Or would you want to send me the info (I would credit you in the response unless you ask me not to - or the general galaxy help email if that is better)? If there isn't a tool, please let us know.
Meanwhile, we are also checking around here for some development programs that *may* do this kind of thing. But obviously an existing Galaxy tool/workflow would be better.
Thanks! And if I should be using someone else as a point person, please let me know and I'll spread the word over here.
We appreciate your help! jen
Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University
Thank you Guru! Jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Guruprasad Ananda" <gua110@bx.psu.edu> wrote:
From: "Guruprasad Ananda" <gua110@bx.psu.edu> To: "Jennifer Jackson" <jen@soe.ucsc.edu> Cc: "Ann Zweig" <ann@soe.ucsc.edu>, "galaxy" <galaxy-user@bx.psu.edu>, "Dan Blankenberg" <dan@bx.psu.edu> Sent: Monday, February 1, 2010 8:19:33 AM GMT -08:00 US/Canada Pacific Subject: Re: Question from UCSC about SNPs and proteins
Hi Jen,
"Mutate Codons with SNPs" tool under "Evolution" section on Galaxy should help to answer this question. If you look at the tool's help section, it explains the required format of the input dataset. The input should have start, end, stop and strand co-ordinates for each of the codons, joined with start, end, stop, strand co-ordinates and observed SNPs for each of the SNPs. If the user has these data in two separate files, he can join them using "Join" tool under "Operate on genomic intervals" section. The output of the tool will consist of codons in the input mutated with the respective SNPs. To check if the changes are synonymous or not, the user can join this output with a tabular file containing the genetic code using "Join two queries" tool under "Join, subtract and group" section.
I hope this answers your questions. Please feel free to email us if you have any further queries. Also, please send any future Galaxy-related questions to our mailing list at galaxy-user@bx.psu.edu.
Thanks! Guru Galaxy team.
On Jan 29, 2010, at 7:54 PM, Jennifer Jackson wrote:
Hi Guru,
We have a question that we do not have a straightforward answer to. After reviewing the tools at Galaxy, I don't see a clear path to the answer, and was hoping you could help. Either to confirm there is no tool or to suggest a dataflow.
This is the thread so far, so you know where we are:
https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021146.html
https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021147.html
https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021148.html
https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021149.html
The short, the user has a list of novel SNPs and wants to know the
change to the protein (perhaps also novel based off genomic). We have a web-mRna translation tool, but the user would then need to do the rest on his own: cut out the coding region, swap in the SNPs, translate via web tool, then analyze against a protein matrix for synonymous or non-syn changes. Protein only so far (although where they are taking it next - structural or functional implications, etc. we don't know - that is beyond the scope of the analysis we support, so far).
Is there a Galaxy tool or workflow that you could suggest? If yes,
should I forward the question on to the galaxy help list? Would that be the right place to send it? Or would you want to send me the info (I would credit you in the response unless you ask me not to - or the general galaxy help email if that is better)? If there isn't a tool, please let us know.
Meanwhile, we are also checking around here for some development
programs that *may* do this kind of thing. But obviously an existing Galaxy tool/workflow would be better.
Thanks! And if I should be using someone else as a point person,
please let me know and I'll spread the word over here.
We appreciate your help! jen
Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University
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Jennifer Jackson