Forget to include the list, :)
From: jzhang <[email protected]<mailto:[email protected]>> Date: Mon, 13 Jun 2011 10:33:02 -0400 To: David Matthews <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Using snp calls to generate a personalised proteome Hi David, Thanks for the detailed clarification. Basically, you start from a "personalized genome" (via changing reference human genome sequence using SNPs detected by deep sequencing), then using this genome to retrieve protein sequences. Although your use case is not supported yet, it is definitely doable using the new BioMart analysis plugin framework which is currently under active development. The idea of this plugin framework is to allow developers to extend BioMart standard data retrieval functionality so that certain process/analysis can be done to the data retrieved from a data source. To provide additional flexibility, it is also possible for a plugged in analysis module to decide what data to retrieve. The use case you presented can be done by modifying the first analysis plugin that is available at http://central.biomart.org/sequence/?gui=Sequence_retrieval&mart=gene_ensembl_sequence. What needs to be added is to allow users to upload the list of SNPs, so that the reference genome sequence can be modified accordingly before producing gene/protein sequences. We will consider supporting your use case, however I am not able to comment on when it will be available. We will update you on this once it's ready for use. Best regards, Junjun From: David Matthews <[email protected]<mailto:[email protected]>> Date: Mon, 13 Jun 2011 08:51:13 -0400 To: jzhang <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Using snp calls to generate a personalised proteome Hi, An output example is difficult for me to provide as I am quite new to this. Basically I want to use the actual sequence of the cells I am working with to generate a list of proteins that exactly match what you would expect the cell to be making. So instead of having a canonical list of human proteins I would have a list of proteins that my cells are making based on the sequence data. I want to use this list to run a high throughput mass spec analysis of the proteins in my cell line and by creating a list of proteins which exactly matches the proteins made as revealed by my deep sequencing I hope to improve my protein identifications list and the confidence of my identifications. So ideally I would hope that by providing details of a snp that leads to an aa change, I could download the actual sequence of the protein that is being made (and not the canonical protein) and potentially improve the quality of my mass spec searches - does that make sense? I imagine that most human snps have been seen already so I kind of hoped the output file would be returned with an additional collumn giving me an accession number corresponding to the protein sequence arising from such a snp... Does that make sense? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 [email protected]<mailto:[email protected]> On 13 Jun 2011, at 13:38, Junjun Zhang wrote: Hi David, You showed us the example input, can you please give an output example so that I understand you request better? Best, Junjun From: David Matthews [mailto:[email protected]] Sent: Monday, June 13, 2011 08:11 AM To: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] Using snp calls to generate a personalised proteome Hi Biomart, I have a human snp list generated by the software "aaChanges" and was wondering if there is a way of using this list to generate a "personalised" human proteome? Here is an example of the file: chr1 888658 888659 C ENST00000327044 Ile:Val 300 T chr1 906258 906259 G/T ENST00000379407 Gly:Gly/Val 162 G chr1 906258 906259 G/T ENST00000379410 Gly:Gly/Val 162 G chr1 906258 906259 G/T ENST00000379409 Gly:Gly/Val 202 G chr1 949607 949608 A/G ENST00000379389 Ser:Asn/Ser 83 G chr1 979381 979382 C/T ENST00000379370 Arg:Arg/Trp 660 C chr1 979381 979382 C/T ENST00000539069 Arg:Arg/Trp 82 C chr1 1019858 1019859 A/G ENST00000437760 Val:Val/Ala 178 A chr1 1154307 1154308 T ENST00000465727 Ser:Asn 198 C chr1 1167766 1167767 A/G ENST00000379198 Gly:Arg/Gly 37 G chr1 1245175 1245176 C/T ENST00000379031 Arg:Arg/Trp 197 C chr1 1249186 1249187 A/G ENST00000528879 Arg:Cys/Arg 273 G chr1 1334474 1334475 C/G ENST00000400809 Thr:Ser/Thr 71 G chr1 1334474 1334475 C/G ENST00000496007 Thr:Ser/Thr 71 G chr1 1334474 1334475 C/G ENST00000481223 Thr:Ser/Thr 71 G chr1 1334474 1334475 C/G ENST00000488340 Thr:Ser/Thr 71 G chr1 1334474 1334475 C/G ENST00000408918 Thr:Ser/Thr 71 G chr1 1334474 1334475 C/G ENST00000425598 Thr:Ser/Thr 71 G chr1 1418444 1418445 C ENST00000378741 Trp:Arg 105 T chr1 1418444 1418445 C ENST00000378736 Trp:Arg 104 T chr1 1424581 1424582 C ENST00000378737 Gln:Pro 224 A chr1 1424582 1424583 T ENST00000378737 Gln:His 224 G chr1 1425635 1425636 A ENST00000378737 Arg:Lys 249 G chr1 1431164 1431165 C/T ENST00000378737 Pro:Pro/Ser 473 C chr1 1431164 1431165 C/T ENST00000308647 Pro:Pro/Ser 639 C chr1 1455651 1455652 G/T ENST00000378756 Ala:Ala/Ser 216 G chr1 1455651 1455652 G/T ENST00000378755 Ala:Ala/Ser 264 G Any thoughts on how I might do this or any alternative approaches I might use? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 [email protected]<mailto:[email protected]>
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
