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1 Inputs:
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2
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3 - A tabular file that contains a column with a peptide sequence and a column with an identifier for a reference sequence
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4 - fasta files for the reference sequences
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5 - gff or gtf for mapping the reference sequences to a genome
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6 - reference genome fasta
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7
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8 Ensembl transcript_id files: Homo_sapiens.GRCh37.71.gtf,GRCh37.fa
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9 transcript gtf+reference
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10 map peptide to 3-frame translation of transcript
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11 map to reference genome with ensembl gtf
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12
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13 ECGene ec_id files: ECgene_hg18_b1_low.fa,GRCh37.fa
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14 transcript from ecgene.fa
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15 map peptide to 3-frame translation of transcript
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16 map transcript to reference genome with blat
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17
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18 Augustus id files: ssc10.2.RNA.hints.augustus.fa, ssc10.2.RNA.hints.augustus.gff
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19 map peptide to augustus protien fasta
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20 map to reference genome with GFF3
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21
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22 EEJ files: Homo_sapiens.GRCh37.71.gtf,eej_sus_scrofa_core_70_102.fa
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23 map peptide to eej fasta
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24 parse id to find exon names and junc_pos
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25 map to reference genome with exon_id in ensembl GTF
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26
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27
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28 Output:
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29 a GFF3 file that specifies the position of the peptide in a reference genome
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30
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31
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32 Mapping:
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33 find transcript in cDNA fasta:
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34 find transcript in translated fasta:
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35
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36
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37 peptide to transcript:
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38 translate transcript to animo acid sequence and search for peptide
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39 tblastn
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40 Biopython
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41
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42 transcript to genome:
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43 If the fasta id lines contain the genomic mapping, use that
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44 Map transcript to reference genome with BLAT
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45 see if peptide cross exon boundaries
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46
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