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"