I am fairly new to bioinformatics and am trying to self teach myself but I have been having trouble acquiring the sequences I want. What I have been trying to do is acquire all variants of a gene's CDS across all mammalian species. First I tried simply BLASTing to acquire my sequences but as I expanded my search, I was getting too much paralog ortholog overlap and I need to separate them from each other, I do intend to look at the paralogs but I need them separate. Next I began trying to learn BiomaRt to write an R script to do what I want, but the data that biomaRt retrieves is in reference sequences and I want all variants from all mammalian species. As for SNP data, it does not give me it in a FASTA of the CDS it just gives me chromosome position, a mutation type and an rfsnp ID, I thought maybe I could put the rfsnp ID into the getSequence function but it does not accept those IDs. I am still trying to learn what the BiomaRt plugin can do or to find some other way to get what I need Can anyone offer some advice? is there an easier way to go about what I am doing or can BiomaRt do something I am unaware of? any advice or solutions would be helpful, especially R advice as I need to work with large amount of data and export them to excel files. Any advice for self teaching myself bioinformatics is appreciated.
