versions of protein sequences from associated transcript sequences

2014-08-29

azim58 - versions of protein sequences from associated transcript
sequences

I have 9 proteins to examine. I want to get the RNA transcripts for these
proteins, and I want to compare sequences against different versions of
these 9 proteins.

Versions of proteins

protein sequence from all 6 reading frames of the whole transcript
-protein_sequence_name_w_rf_1-6 where w indicates "whole transcript", rf

indicates "reading frame", and 1-3 indicates the forward reading frames
1-3 and 4-6 indicates the reverse reading frames 4-6.

protein sequence from all 3 reading frames from the normal start codon

of the transcript

-protein_sequence_name_fs_rf_1-3 where w indicates fs indicates "from

start codon", rf indicates "reading frame", and 1-3 indicates reading
frames 1-3

so each transcript will have 9 protein sequences associated with it

Excel Sheet
"C:\kurt\storage\CIM Research Folder\DR\2013\3-30-13\sequence
analysis\versions of protein sequences from associated transcript
sequences 3-30-13.xlsx"

fasta file of all of the versions of the protein sequences
C:\kurt\storage\CIM Research Folder\DR\2013\3-30-13\sequence
analysis\versions of protein sequences from associated transcript
sequences 3-30-13.fa
shorter name here
"C:\kurt\storage\CIM Research Folder\DR\2013\3-30-13\sequence
analysis\prot_3-30-13.fa"

fasta file just from the start codon
"C:\kurt\storage\CIM Research Folder\DR\2013\3-30-13\sequence
analysis\prot_fs_4-1-13.fa"