Hi, I have downloaded and am looking at the refGene.exonAA.fa file for the 46 multizway alignment. I am trying to match each amino acid to its corresponding 3 nucleotide position. I realize this is the meaning of the header and sequence:
>Name_Assembly(Species)_Exon#_TotalExons ExonLength(AA) InFrame OutFrame Location Strand(+/-) AASequence example: >NM_032291_hg19_1_25 3 0 1 chr1:67000042-67000051+ MME What I’m trying to determine is if I have the rules right for assigning location. Can anyone confirm this? Rules I figured based on looking at examples in the file: Assume given location chr:a-b 1. * If strand is + a. if inframe is 0 than first amino acid is equal to chr:a, chr:a +1, chr:a+2 b. if inframe is 1 than first amino acid is equal to chr:a-1, chr:a, chr:a+1 c. if inframe is 2 than first amino acid is equal to chr:a+1, chr:a+2, chr:a+3 2. *if strand is – a. if inframe is 0 than first amino acid is equal to chr:b, chr:b-1, chr:b-2 b. if inframe is 1 than first amino acid is equal to chr:b+1, chr:b, chr:b-1 c. if inframe is 2 than first amino acid is equal to chr:b-1, chr:b-2, chr:b-3 Please let me know if these are correct assumptions or not. Thank you. Tychele _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
