Add ecoli reference files for EpitopeID

owlang · owlang · commit 032a44919f00 · 2021-11-17T13:31:54.000-05:00
This commit includes the reference files for running EpitopeID on E. coli data using the W3110 strain reference assembly. The utility scripts are also updated to allow users to rebuild the annotation files with different bin sizes. The .gitignore file was updated to exclude the BWA index files but the ecoli genome (small file size) is included in this commit.
diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,11 @@ EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.ann
 EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.bwt
 EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.pac
 EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.sa
+EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.amb
+EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.ann
+EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.bwt
+EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.pac
+EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.sa
 EpitopeID/hg19_EpiID/FASTA_genome/genome.fa
 EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.amb
 EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.ann
diff --git a/EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa b/EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa
diff --git a/EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.fai b/EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.fai
@@ -0,0 +1 @@
+W3110	4646332	7	70	71
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa
@@ -0,0 +1,26 @@
+>AID
+CCAAAAGATCCGGCGAAGCCACCCGCGAAGGCGCAGGTTGTTGGTTGGCCACCTGTAAGGTCATATCGTAAGAATGTTATGGTTAGCTGTCAGAAGAGCAGTGGCGGTCCAGAGGCCGCTGCATTTGTGAAA
+>CBP
+AAGAGAAGGTGGAAGAAGAACTTCATCGCCGTGAGCGCGGCAAACCGTTTCAAGAAGATAAGTAGCAGTGGAGCATTA
+>Extended-Tap
+GGTCGACGGATCCCCGGGTTAATTAATCCATGGAAGAGAAGATGGAAAAAGAATTTCATAGCCGTCTCAGCAGCCAACCGCTTTAAGAAAATCTCATCCTCCGGGGCACTTGATTATGATATTCCAACTACTGCTAGCGAGAATTTGTATTTTCAGGGAGAATTCGGCCTTGCGCAACACGATGAAGCCGTGGACAACAAATTCAACAAAGAACAACAAAACGCGTTCTATGAGATCTTACATTTACCTAACTTAAACGAAGAACAACGAAACGCCTTCATCCAAAGTTTAAAAGATGACCCAAGCCAAAGCGCTAACCTTTTAGCAGAAGCTAAAAAGCTAAATGATGCTCAGGCGCCGAAAGTAGACAACAAATTCAACAAAGAACAACAAAACGCGTTCTATGAGATCTTACATTTACCTAACTTAAACGAAGAACAACGAAACGCCTTCATCCAAAGTTTAAAAGATGACCCAAGCCAAAGCGCTAACCTTTTAGCAGAAGCTAAAAAGCTAAATGATGCTCAGGCGCCGAAAGTAGACGCGAATCATCAGTGAGGCGCGCCACTTCTAAATAAGCGAATTTCTTATGATTTATGATTTTTATTATTAAATAAGTTATAAAAAAAATAAGTGTATACAAATTTTAAAGTGACTCTTAGGTTTTAAAACGAAAATTCTTATTCTTGAGTAACTCTTTCCTGTAGGTCAGGTTGCTTTCTCAGGTATAGTATGAGGTCGCTCTTATTGACCACACCTCTACCGGCAGATCCGCTAGGGATAACAGGGTAATATAGATCTGTTTAGCTTGCCTCGTCCCCGCCGGGTCACCCGGCCAGCGACATGGAGGCCCAGAATACCCTCCTTGACAGTCTTGACGTGCGCAGCTCAGGGGCATGATGTGACTGTCGCCCGTACATTTAGCCCATACATCCCCATGTATAATCATTTGCATCCATACATTTTGATGGCCGCACGGCGCGAAGCAAAAATTACGGCTCCTCGCTGCAGACCTGCGAGCAGGGAAACGCTCCCCTCACAGACGCGTTGAATTGTCCCCACGCCGCGCCCCTGTAGAGAAATATAAAAGGTTAGGATTTGCCACTGAGGTTCTTCTTTCATATACTTCCTTTTAAAATCTTGCTAGGATACAGTTCTCACATCACATCCGAACATAAACAACCATGGGTAGGAGGGCTTTTGTAGAAAGAAATACGAACGAAACGAAAATCAGCGTTGCCATCGCTTTGGACAAAGCTCCCTTACCTGAAGAGTCGAATTTTATTGATGAACTTATAACTTCCAAGCATGCAAACCAAAAGGGAGAACAAGTAATCCAAGTAGACACGGGAATTGGATTCTTGGATCACATGTATCATGCACTGGCTAAACATGCAGGCTGGAGCTTACGACTTTACTCAAGAGGTGATTTAATCATCGATGATCATCACACTGCAGAAGATACTGCTATTGCACTTGGTATTGCATTCAAGCAGGCTATGGGTAACTTTGCCGGCGTTAAAAGATTTGGACATGCTTATTGTCCACTTGACGAAGCTCTTTCTAGAAGCGTAGTTGACTTGTCGGGACGGCCCTATGCTGTTATCGATTTGGGATTAAAGCGTGAAAAGGTTGGGGAATTGTCCTGTGAAATGATCCCTCACTTACTATATTCCTTTTCGGTAGCAGCTGGAATTACTTTGCATGTTACCTGCTTATATGGTAGTAATGACCATCATCGTGCTGAAAGCGCTTTTAAATCTCTGGCTGTTGCCATGCGCGCGGCTACTAGTCTTACTGGAAGTTCTGAAGTCCCAAGCACGAAGGGAGTGTTGTAAAGAGTACTGACAATAAAAAGATTCTTGTTTTCAAGAACTTGTCATTTGTATAGTTTTTTTATATTGTAGTTGTTCTATTTTAATCAAATGTTAGCGTGATTTATATTTTTTTTCGCCTCGACATCATCTGCCCAGATGCGAAGTTAAGTGCGCAGAAAGTAATATCATGCGTCAATCGTATGTGAATGCTGGTCGCTATACTGCTGTCGATTCGATACTAACGCCGCCATCCAGTTTAAACGAGCTCGAATTCATCGA
+>FLAG-3x
+AGATTACAAGGATCACGATGGCGATTACAAGGATCACGATATCGATTACAAGGATGATGATGATAAG
+>FRB
+ATATTGTGGCACGAGATGTGGCACGAAGGGCTGGAAGAGGCCTCTAGGCTATACTTTGGCGAGCGTAATGTCAAAGGGATGTTCGAGGTGCTAGAGCCCCTTCACGCGATGATGGAGAGAGGTCCACAGACTCTGAAAGAAACGAGCTTCAATCAAGCCTACGGTAGGGACTTGATGGAAGCTCAAGAGTGGTGTCGTAAGTATATGAAATCCGGGAACGTCAAAGACTTGTTACAAGCTTGGGATCTGTATTACCATGTCTTCCGTAGAATCAGCAAG
+>GFP
+GTAAAGGTGAGGAATTATTTACAGGCGTAGTACCAATCCTAGTAGAGTTAGACGGCGACGTCAATGGCCACAAATTTAGTGTCTCTGGCGAGGGTGAAGGTGATGCTACCTACGGTAAGTTAACGCTAAAATTTATATGCACTACGGGTAAATTACCAGTACCGTGGCCCACATTAGTGACAACTTTTACTTATGGAGTGCAGTGTTTTTCCCGTTACCCGGATCACATGAAAAGGCACGACTTCTTCAAATCTGCTATGCCGGAAGGGTACGTTCAAGAAAGAACTATATTTTTTAAGGACGACGGGAATTACAAGACCAGAGCTGAAGTAAAATTTGAGGGAGACACCTTGGTTAACAGAATTGAGCTAAAGGGAATAGATTTCAAAGAAGATGGGAACATCCTAGGCCATAAATTAGAGTACAACTATAATTCACACAATGTGTATATAATGGCAGATAAGCAGAAAAATGGAATTAAAGTTAACTTCAAGATTAGACACAATATCGAAGATGGGAGTGTCCAGCTAGCCGATCACTATCAACAGAATACGCCGATTGGCGATGGGCCTGTCCTTTTGCCAGATAATCACTATCTTTCTACACAATCTGCTCTGAGTAAGGACCCGAATGAGAAACGTGACCACATGGTCCTGTTGGAATTTGTAACAGCAGCGGGCATAACACACGGCATGGATGAGCTATATAAA
+>HA_v1
+TACCCATACGATGTTCCAGATTACGCTTACCCATACGATGTTCCAGATTACGCTTACCCATACGATGTTCCAGATTACGCT
+>HA_v2
+TATCCATATGATGTTCCAGATTATGCTTATCCATATGATGTTCCAGATTATGCTTATCCATATGATGTTCCAGATTATGCT
+>HA_v3
+GCGGCCGTTTACCCATACGATGTTCCTGACTATGCGGGCTATCCCTATGACGTCCCGGACTATGCAGGATCCTATCCATATGACGTTCCAGATTACGCTCCGGCCGCC
+>HaloTag
+AATGCAGAAATAGGGACAGGCTTTCCTTTTGATCCCCATTATGTAGAGGTACTAGGAGAACGTATGCATTACGTGGACGTGGGACCAAGAGATGGCACCCCAGTTCTTTTTTTACACGGAAACCCAACCAGTTCTTATGTCTGGAGGAACATCATCCCTCACGTTGCTCCAACTCACAGATGTATAGCGCCTGATCTGATTGGGATGGGTAAATCAGACAAACCCGACTTGGGCTACTTCTTCGATGACCACGTCAGATTTATGGACGCGTTCATTGAGGCACTTGGGTTGGAAGAAGTCGTCCTGGTAATACATGACTGGGGATCAGCCCTGGGATTTCATTGGGCTAAAAGGAATCCAGAGAGAGTAAAAGGGATTGCCTTCATGGAGTTTATCAGGCCCATACCCACCTGGGATGAGTGGCCCGAGTTTGCTAGAGAGACCTTCCAGGCTTTCAGGACTACCGATGTCGGCCGTAAATTGATTATTGACCAAAATGTTTTCATCGAGGGAACGTTGCCTATGGGCGTAGTCCGTCCCCTAACGGAGGTCGAAATGGATCATTACAGAGAACCGTTTTTGAACCCTGTAGACCGTGAGCCACTGTGGCGTTTTCCAAACGAATTACCGATAGCTGGCGAACCCGCTAATATCGTCGCCCTGGTAGAGGAATACATGGACTGGCTTCATCAAAGTCCTGTTCCCAAATTGTTATTTTGGGGTACACCAGGTGTATTAATTCCACCTGCCGAAGCCGCCAGGTTGGCAAAATCATTACCGAACTGCAAAGCTGTAGACATCGGCCCCGGTTTGAATCTGCTGCAGGAGGATAACCCGGATTTGATAGGGTCTGAAATCGCGCGTTGGTTGTCAACCCTGGAAATATCAGGC
+>MNase_v2
+CCGCCACCAGTACCAAGAAGCTGCACAAGGAGCCCGCCACCCTGATCAAGGCCATAGATGGCGATACCGTGAAGCTGATGTATAAGGGCCAGCCCATGACCTTCCGCCTGCTGCTGGTGGATACCCCCGAGACCAAGCACCCGAAAAAGGGCGTGGAAAAGTACGGACCCGAGGCCAGCGCCTTCACAAAAAAGATGGTGGAGAACGCCAAGAAAATCGAGGTGGAGTTCGATAAAGGCCAACGCACCGATAAGTATGGACGCGGTCTGGCCTACATCTACGCCGACGGCAAAATGGTGAACGAGGCCCTGGTGCGGCAGGGACTGGCCAAGGTGGCGTACGTGTACAAGCCCAACAACACCCACGAGCAGCACCTGCGCAAGAGCGAGGCTCAGGCAAAGAAGGAGAAACTGAACATCTGGAGTGAGGATAACGCCGATAGCGGCCAGT
+>Myc-3x
+GGCGAACAGAAGCTAATCAGTGAGGAGGACCTTAATGGTGAGCAGAAACTAATCTCTGAAGAGGATTTGAATGGAGAACAAAAGCTGATTTCTGAGGAGGACTTAAAC
+>ProteinA
+AAAACGGCAGCTTTAGCGCAGCACGACGAGGCTGTGGACAATAAGTTTAACAAGGAGCAGCAGAACGCATTCTACGAGATCCTTCATCTGCCTAACCTGAATGAGGAACAAAGGAACGCGTTCATTCAAAGTCTGAAGGACGACCCAAGCCAGTCAGCGAATTTGCTTGCCGAAGCAAAAAAACTGAACGACGCCCAAGCGCCCAAAGTCGATAATAAATTCAATAAGGAACAGCAGAATGCATTCTATGAGATTCTGCATCTACCGAATCTTAACGAAGAACAGAGGAACGCCTTTATCCAGTCTCTAAAGGATGATCCAAGCCAATCCGCTAACCTATTAGCTGAAGCAAAGAAGCTTAATGGAGCCCAAGCACCGAAAGTTGATGCCAACAGTGCCGGTAAATCAACT
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.amb b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.amb
@@ -0,0 +1 @@
+5492 13 0
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.ann b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.ann
@@ -0,0 +1,27 @@
+5492 13 11
+0 AID (null)
+0 132 0
+0 CBP (null)
+132 78 0
+0 Extended-Tap (null)
+210 2096 0
+0 FLAG-3x (null)
+2306 67 0
+0 FRB (null)
+2373 279 0
+0 GFP (null)
+2652 710 0
+0 HA_v1 (null)
+3362 81 0
+0 HA_v2 (null)
+3443 81 0
+0 HA_v3 (null)
+3524 108 0
+0 HaloTag (null)
+3632 891 0
+0 MNase_v2 (null)
+4523 450 0
+0 Myc-3x (null)
+4973 108 0
+0 ProteinA (null)
+5081 411 0
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.bwt b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.bwt
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.pac b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.pac
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.sa b/EpitopeID/ecoli_EpiID/FASTA_tag/ALL_TAG.fa.sa
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/AID.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/AID.fa
@@ -0,0 +1,2 @@
+>AID
+CCAAAAGATCCGGCGAAGCCACCCGCGAAGGCGCAGGTTGTTGGTTGGCCACCTGTAAGGTCATATCGTAAGAATGTTATGGTTAGCTGTCAGAAGAGCAGTGGCGGTCCAGAGGCCGCTGCATTTGTGAAA
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/CBP.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/CBP.fa
@@ -0,0 +1,2 @@
+>CBP
+AAGAGAAGGTGGAAGAAGAACTTCATCGCCGTGAGCGCGGCAAACCGTTTCAAGAAGATAAGTAGCAGTGGAGCATTA
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/Extended-Tap.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/Extended-Tap.fa
@@ -0,0 +1,2 @@
+>Extended-Tap
+GGTCGACGGATCCCCGGGTTAATTAATCCATGGAAGAGAAGATGGAAAAAGAATTTCATAGCCGTCTCAGCAGCCAACCGCTTTAAGAAAATCTCATCCTCCGGGGCACTTGATTATGATATTCCAACTACTGCTAGCGAGAATTTGTATTTTCAGGGAGAATTCGGCCTTGCGCAACACGATGAAGCCGTGGACAACAAATTCAACAAAGAACAACAAAACGCGTTCTATGAGATCTTACATTTACCTAACTTAAACGAAGAACAACGAAACGCCTTCATCCAAAGTTTAAAAGATGACCCAAGCCAAAGCGCTAACCTTTTAGCAGAAGCTAAAAAGCTAAATGATGCTCAGGCGCCGAAAGTAGACAACAAATTCAACAAAGAACAACAAAACGCGTTCTATGAGATCTTACATTTACCTAACTTAAACGAAGAACAACGAAACGCCTTCATCCAAAGTTTAAAAGATGACCCAAGCCAAAGCGCTAACCTTTTAGCAGAAGCTAAAAAGCTAAATGATGCTCAGGCGCCGAAAGTAGACGCGAATCATCAGTGAGGCGCGCCACTTCTAAATAAGCGAATTTCTTATGATTTATGATTTTTATTATTAAATAAGTTATAAAAAAAATAAGTGTATACAAATTTTAAAGTGACTCTTAGGTTTTAAAACGAAAATTCTTATTCTTGAGTAACTCTTTCCTGTAGGTCAGGTTGCTTTCTCAGGTATAGTATGAGGTCGCTCTTATTGACCACACCTCTACCGGCAGATCCGCTAGGGATAACAGGGTAATATAGATCTGTTTAGCTTGCCTCGTCCCCGCCGGGTCACCCGGCCAGCGACATGGAGGCCCAGAATACCCTCCTTGACAGTCTTGACGTGCGCAGCTCAGGGGCATGATGTGACTGTCGCCCGTACATTTAGCCCATACATCCCCATGTATAATCATTTGCATCCATACATTTTGATGGCCGCACGGCGCGAAGCAAAAATTACGGCTCCTCGCTGCAGACCTGCGAGCAGGGAAACGCTCCCCTCACAGACGCGTTGAATTGTCCCCACGCCGCGCCCCTGTAGAGAAATATAAAAGGTTAGGATTTGCCACTGAGGTTCTTCTTTCATATACTTCCTTTTAAAATCTTGCTAGGATACAGTTCTCACATCACATCCGAACATAAACAACCATGGGTAGGAGGGCTTTTGTAGAAAGAAATACGAACGAAACGAAAATCAGCGTTGCCATCGCTTTGGACAAAGCTCCCTTACCTGAAGAGTCGAATTTTATTGATGAACTTATAACTTCCAAGCATGCAAACCAAAAGGGAGAACAAGTAATCCAAGTAGACACGGGAATTGGATTCTTGGATCACATGTATCATGCACTGGCTAAACATGCAGGCTGGAGCTTACGACTTTACTCAAGAGGTGATTTAATCATCGATGATCATCACACTGCAGAAGATACTGCTATTGCACTTGGTATTGCATTCAAGCAGGCTATGGGTAACTTTGCCGGCGTTAAAAGATTTGGACATGCTTATTGTCCACTTGACGAAGCTCTTTCTAGAAGCGTAGTTGACTTGTCGGGACGGCCCTATGCTGTTATCGATTTGGGATTAAAGCGTGAAAAGGTTGGGGAATTGTCCTGTGAAATGATCCCTCACTTACTATATTCCTTTTCGGTAGCAGCTGGAATTACTTTGCATGTTACCTGCTTATATGGTAGTAATGACCATCATCGTGCTGAAAGCGCTTTTAAATCTCTGGCTGTTGCCATGCGCGCGGCTACTAGTCTTACTGGAAGTTCTGAAGTCCCAAGCACGAAGGGAGTGTTGTAAAGAGTACTGACAATAAAAAGATTCTTGTTTTCAAGAACTTGTCATTTGTATAGTTTTTTTATATTGTAGTTGTTCTATTTTAATCAAATGTTAGCGTGATTTATATTTTTTTTCGCCTCGACATCATCTGCCCAGATGCGAAGTTAAGTGCGCAGAAAGTAATATCATGCGTCAATCGTATGTGAATGCTGGTCGCTATACTGCTGTCGATTCGATACTAACGCCGCCATCCAGTTTAAACGAGCTCGAATTCATCGA
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/FLAG-3x.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/FLAG-3x.fa
@@ -0,0 +1,2 @@
+>FLAG-3x
+AGATTACAAGGATCACGATGGCGATTACAAGGATCACGATATCGATTACAAGGATGATGATGATAAG
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/FRB.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/FRB.fa
@@ -0,0 +1,2 @@
+>FRB
+ATATTGTGGCACGAGATGTGGCACGAAGGGCTGGAAGAGGCCTCTAGGCTATACTTTGGCGAGCGTAATGTCAAAGGGATGTTCGAGGTGCTAGAGCCCCTTCACGCGATGATGGAGAGAGGTCCACAGACTCTGAAAGAAACGAGCTTCAATCAAGCCTACGGTAGGGACTTGATGGAAGCTCAAGAGTGGTGTCGTAAGTATATGAAATCCGGGAACGTCAAAGACTTGTTACAAGCTTGGGATCTGTATTACCATGTCTTCCGTAGAATCAGCAAG
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/GFP.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/GFP.fa
@@ -0,0 +1,2 @@
+>GFP
+GTAAAGGTGAGGAATTATTTACAGGCGTAGTACCAATCCTAGTAGAGTTAGACGGCGACGTCAATGGCCACAAATTTAGTGTCTCTGGCGAGGGTGAAGGTGATGCTACCTACGGTAAGTTAACGCTAAAATTTATATGCACTACGGGTAAATTACCAGTACCGTGGCCCACATTAGTGACAACTTTTACTTATGGAGTGCAGTGTTTTTCCCGTTACCCGGATCACATGAAAAGGCACGACTTCTTCAAATCTGCTATGCCGGAAGGGTACGTTCAAGAAAGAACTATATTTTTTAAGGACGACGGGAATTACAAGACCAGAGCTGAAGTAAAATTTGAGGGAGACACCTTGGTTAACAGAATTGAGCTAAAGGGAATAGATTTCAAAGAAGATGGGAACATCCTAGGCCATAAATTAGAGTACAACTATAATTCACACAATGTGTATATAATGGCAGATAAGCAGAAAAATGGAATTAAAGTTAACTTCAAGATTAGACACAATATCGAAGATGGGAGTGTCCAGCTAGCCGATCACTATCAACAGAATACGCCGATTGGCGATGGGCCTGTCCTTTTGCCAGATAATCACTATCTTTCTACACAATCTGCTCTGAGTAAGGACCCGAATGAGAAACGTGACCACATGGTCCTGTTGGAATTTGTAACAGCAGCGGGCATAACACACGGCATGGATGAGCTATATAAA
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HA_v1.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HA_v1.fa
@@ -0,0 +1,2 @@
+>HA_v1
+TACCCATACGATGTTCCAGATTACGCTTACCCATACGATGTTCCAGATTACGCTTACCCATACGATGTTCCAGATTACGCT
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HA_v2.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HA_v2.fa
@@ -0,0 +1,2 @@
+>HA_v2
+TATCCATATGATGTTCCAGATTATGCTTATCCATATGATGTTCCAGATTATGCTTATCCATATGATGTTCCAGATTATGCT
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HA_v3.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HA_v3.fa
@@ -0,0 +1,2 @@
+>HA_v3
+GCGGCCGTTTACCCATACGATGTTCCTGACTATGCGGGCTATCCCTATGACGTCCCGGACTATGCAGGATCCTATCCATATGACGTTCCAGATTACGCTCCGGCCGCC
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HaloTag.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/HaloTag.fa
@@ -0,0 +1,2 @@
+>HaloTag
+AATGCAGAAATAGGGACAGGCTTTCCTTTTGATCCCCATTATGTAGAGGTACTAGGAGAACGTATGCATTACGTGGACGTGGGACCAAGAGATGGCACCCCAGTTCTTTTTTTACACGGAAACCCAACCAGTTCTTATGTCTGGAGGAACATCATCCCTCACGTTGCTCCAACTCACAGATGTATAGCGCCTGATCTGATTGGGATGGGTAAATCAGACAAACCCGACTTGGGCTACTTCTTCGATGACCACGTCAGATTTATGGACGCGTTCATTGAGGCACTTGGGTTGGAAGAAGTCGTCCTGGTAATACATGACTGGGGATCAGCCCTGGGATTTCATTGGGCTAAAAGGAATCCAGAGAGAGTAAAAGGGATTGCCTTCATGGAGTTTATCAGGCCCATACCCACCTGGGATGAGTGGCCCGAGTTTGCTAGAGAGACCTTCCAGGCTTTCAGGACTACCGATGTCGGCCGTAAATTGATTATTGACCAAAATGTTTTCATCGAGGGAACGTTGCCTATGGGCGTAGTCCGTCCCCTAACGGAGGTCGAAATGGATCATTACAGAGAACCGTTTTTGAACCCTGTAGACCGTGAGCCACTGTGGCGTTTTCCAAACGAATTACCGATAGCTGGCGAACCCGCTAATATCGTCGCCCTGGTAGAGGAATACATGGACTGGCTTCATCAAAGTCCTGTTCCCAAATTGTTATTTTGGGGTACACCAGGTGTATTAATTCCACCTGCCGAAGCCGCCAGGTTGGCAAAATCATTACCGAACTGCAAAGCTGTAGACATCGGCCCCGGTTTGAATCTGCTGCAGGAGGATAACCCGGATTTGATAGGGTCTGAAATCGCGCGTTGGTTGTCAACCCTGGAAATATCAGGC
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/MNase.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/MNase.fa
@@ -0,0 +1,2 @@
+>MNase_v2
+CCGCCACCAGTACCAAGAAGCTGCACAAGGAGCCCGCCACCCTGATCAAGGCCATAGATGGCGATACCGTGAAGCTGATGTATAAGGGCCAGCCCATGACCTTCCGCCTGCTGCTGGTGGATACCCCCGAGACCAAGCACCCGAAAAAGGGCGTGGAAAAGTACGGACCCGAGGCCAGCGCCTTCACAAAAAAGATGGTGGAGAACGCCAAGAAAATCGAGGTGGAGTTCGATAAAGGCCAACGCACCGATAAGTATGGACGCGGTCTGGCCTACATCTACGCCGACGGCAAAATGGTGAACGAGGCCCTGGTGCGGCAGGGACTGGCCAAGGTGGCGTACGTGTACAAGCCCAACAACACCCACGAGCAGCACCTGCGCAAGAGCGAGGCTCAGGCAAAGAAGGAGAAACTGAACATCTGGAGTGAGGATAACGCCGATAGCGGCCAGT
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/Myc-3x.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/Myc-3x.fa
@@ -0,0 +1,2 @@
+>Myc-3x
+GGCGAACAGAAGCTAATCAGTGAGGAGGACCTTAATGGTGAGCAGAAACTAATCTCTGAAGAGGATTTGAATGGAGAACAAAAGCTGATTTCTGAGGAGGACTTAAAC
diff --git a/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/ProtA.fa b/EpitopeID/ecoli_EpiID/FASTA_tag/Tag_DB/ProtA.fa
@@ -0,0 +1,2 @@
+>ProteinA
+AAAACGGCAGCTTTAGCGCAGCACGACGAGGCTGTGGACAATAAGTTTAACAAGGAGCAGCAGAACGCATTCTACGAGATCCTTCATCTGCCTAACCTGAATGAGGAACAAAGGAACGCGTTCATTCAAAGTCTGAAGGACGACCCAAGCCAGTCAGCGAATTTGCTTGCCGAAGCAAAAAAACTGAACGACGCCCAAGCGCCCAAAGTCGATAATAAATTCAATAAGGAACAGCAGAATGCATTCTATGAGATTCTGCATCTACCGAATCTTAACGAAGAACAGAGGAACGCCTTTATCCAGTCTCTAAAGGATGATCCAAGCCAATCCGCTAACCTATTAGCTGAAGCAAAGAAGCTTAATGGAGCCCAAGCACCGAAAGTTGATGCCAACAGTGCCGGTAAATCAACT
diff --git a/EpitopeID/ecoli_EpiID/annotation/genome_annotation.gff.gz b/EpitopeID/ecoli_EpiID/annotation/genome_annotation.gff.gz
diff --git a/EpitopeID/ecoli_EpiID/blacklist_filter/blacklist.bed b/EpitopeID/ecoli_EpiID/blacklist_filter/blacklist.bed
@@ -0,0 +1 @@
+chrZ	1	2	none	.	-
diff --git a/EpitopeID/utility_scripts/annotation_data/ORF/ec2_W3110_annotation.gff b/EpitopeID/utility_scripts/annotation_data/ORF/ec2_W3110_annotation.gff
diff --git a/EpitopeID/utility_scripts/annotation_data/generate_W3110_GenomeAnnotation.sh b/EpitopeID/utility_scripts/annotation_data/generate_W3110_GenomeAnnotation.sh
diff --git a/EpitopeID/utility_scripts/annotation_data/parsers/parse_W3110_ORF_GFF.pl b/EpitopeID/utility_scripts/annotation_data/parsers/parse_W3110_ORF_GFF.pl

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+>AID`
	`2`	`+CCAAAAGATCCGGCGAAGCCACCCGCGAAGGCGCAGGTTGTTGGTTGGCCACCTGTAAGGTCATATCGTAAGAATGTTATGGTTAGCTGTCAGAAGAGCAGTGGCGGTCCAGAGGCCGCTGCATTTGTGAAA`