hmmalign with --outformat a2m discards padding #345
Description
Tested with HMMER 3.4.
Using hmmalign with --outformat a2m discards the padding from the FASTA output, which means it cannot be loaded back. Example with the given DNA sequences and HMM:
hmmalign --outformat a2m 16S.hmm 16S.fna
Output:
Details
>NC_016617:538069..539152 ttgaac----CTGAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCATGCCTAACAC ATGCAAGTCGAACGAGG-----GCTTCGGC------CCTAGTGGCGCACGGGTGAGTAAC ACGTGGGA-ACCTGCCTTTCGGTTCGGGATAACGTCTGGAAACGGACGCTAACACCGGAT ACG-------TCCTTCGGGA-------GAAAGTT-----TACGCCGAGAGAGGGGCCCGC GTCCGATTAGGTAGTTGGTGGGGTAATGGCCCACCAAGCCGACGATCGGTAGCTGGTCTG AGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAG TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGAGTGATGAAGG CCTTAGGGTTGTAAAGCTCTTTCGCACGCGACGATG-A-----------------TGACG GTAGCGTGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGG CGAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCTGTTTAGTCAGAAG TGAAAGCCCCGGGCTTAACCTGGGAACGGCTTTTGATACTGGCAGGCTTGAGTTCCGGAG AGGATGGTGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCGGTG GCGAAGGCGGCCATCTGGACGGACACCTACGACGAGGCGCGAAAGCGTGGGGAGCAAACA GGATTAGATACCCTGCTAGTGCCCGCGGTAAACGATTAATCCTAAACGATGGGGTGC-AT GCACTTCGGTGTGGACATTAACCCAGTAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGT TCAAACTCAAATGAATTGACGGGGGCACGCACAAGCGATCGAGCATGAGGTCTAAGTGGA AGCAACGTGCAGAACCATACCAACCCAGGACACGCACGAcaCCGGCACCAGAGAGGGAGG GAaCAGCTCCGGAGGGAGGAACACAGGCGCCCCATGACGGTCGACAGCTGGTGTGGCGAG AGTCAGGGATAAGTCGAGCATGCAGCCCAAACCCTTCAGCCAGTTTCCATCC-------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------tgcgg >NC_016594:913476..914972 ttgaac----CTGAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCATGCCTAACAC ATGCAAGTCGAACGAAG-----GCTTCGGC------CTTAGTGGCGCACGGGTGAGTAAC ACGTGGGA-ACCTGCCTTTCGGTTCGGGATAACGTCTGGAAACGGACGCTAACACCGGAT ACG-------TCCTTCGGGA-------GAAAGTT-----TACGCCGAGAGAGGGGCCCGC GTCCGATTAGGTAGTTGGTGGGGTAATGGCCCACCAAGCCGACGATCGGTAGCTGGTCTG AGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAG TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGAGTGATGAAGG CCTTAGGGTTGTAAAGCTCTTTCGCACGCGACGATG-A-----------------TGACG GTAGCGTGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGG CGAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCTGTTTAGTCAGAAG TGAAAGCCCCGGGCTTAACCTGGGAACGGCTTTTGATACTGGCAGGCTTGAGTTCCGGAG AGGATGGTGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTGGGAAGAACACCGGTG GCGAAGGCGGCCATCTGGACGGACACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACA GGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATGCTAGACGCTGGGGTGC-AT GCACTTCGGTGTCGCCGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGT TAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGA AGCAACGCGCAGAACCTTACCAACCCTTGACATGTCCACcaCCGGCTCCAGAGATGGAGC TTTCAGTTcGGCTGGGTGGAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAG ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTACCGCCAGTTGCCATCAT-TC-AGT TGGGCACTCTGGTGGAACTGCCGGTGACAAGCCGGAGGAAGGCGGGGATGACGTCAAGTC CTCATGGCCCTTATGGGTTGGGCTACACACGTGCTACAATGGCGGTGACAGTGGGATGCG AAGTCGCAAGATGGAGCCAATCCCC-AAAAGCCGTCTCAGTTCGGATTGCACTCTGCAAC TCGGGTGCATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGT TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGCTTTACCCGAAGGTGGT GCGCTAACCcGCAAgGGAGGCAGCCAACCACGGTCAGGTCAGCGACTGGGGTGAAGTCGT AACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTT-tctaaggaaa >NC_016594:1099329..1100825 tgaac----CTGAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCATGCCTAACACA TGCAAGTCGAACGAGG-----GCTTCGGC------CCTAGTGGCGCACGGGTGAGTAACA CGTGGGA-ACCTGCCTTTCGGTTCGGGATAACGTCTGGAAACGGACGCTAACACCGGATA CG-------TCCTTCGGGA-------GAAAGTT-----TACGCCGAGAGAGGGGCCCGCG TCCGATTAGGTAGTTGGTGGGGTAATGGCCCACCAAGCCGACGATCGGTAGCTGGTCTGA GAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGT GGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGC CTTAGGGTTGTAAAGCTCTTTCGCACGCGACGATG-A-----------------TGACGG TAGCGTGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGC GAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCTGTTTAGTCAGAAGT GAAAGCCCCGGGCTTAACCTGGGAACGGCTTTTGATACTGGCAGGCTTGAGTTCCGGAGA GGATGGTGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTGGGAAGAACACCGGTGG CGAAGGCGGCCATCTGGACGGACACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAG GATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATGCTAGACGCTGGGGTGC-ATG CACTTCGGTGTCGCCGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGTT AAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAA GCAACGCGCAGAACCTTACCAACCCTTGACATGTCCACcaCCGGCTCCAGAGATGGAGCT TTCAGTTcGGCTGGGTGGAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGA TGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTACCGCCAGTTGCCATCAT-TC-AGTT GGGCACTCTGGTGGAACTGCCGGTGACAAGCCGGAGGAAGGCGGGGATGACGTCAAGTCC TCATGGCCCTTATGGGTTGGGCTACACACGTGCTACAATGGCGGTGACAGTGGGACGCGA AGTCGCAAGATGGAGCCAATCCCC-AAAAGCCGTCTCAGTTCGGATTGCACTCTGCAACT CGGGTGCATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTT CCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGCTTTACCCGAAGGTGGTG CGCTAACCgGCAAcGGAGGCAGCCAACCACGGTCAGGTCAGCGACTGGGGTGAAGTCGTA ACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTT-tctaaggaaaa >NC_016594:1578551..1580047 tgaac----CTGAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCATGCCTAACACA TGCAAGTCGAACGAAG-----GCTTCGGC------CTTAGTGGCGCACGGGTGAGTAACA CGTGGGA-ACCTGCCTTTCGGTTCGGGATAACGTCTGGAAACGGACGCTAACACCGGATA CG-------TCCTTCGGGA-------GAAAGTT-----TACGCCGAGAGAGGGGCCCGCG TCCGATTAGGTAGTTGGTGGGGTAATGGCCCACCAAGCCGACGATCGGTAGCTGGTCTGA GAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGT GGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGC CTTAGGGTTGTAAAGCTCTTTCGCACGCGACGATG-A-----------------TGACGG TAGCGTGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGC GAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCTGTTTAGTCAGAAGT GAAAGCCCCGGGCTTAACCTGGGAACGGCTTTTGATACTGGCAGGCTTGAGTTCCGGAGA GGATGGTGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTGGGAAGAACACCGGTGG CGAAGGCGGCCATCTGGACGGACACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAG GATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATGCTAGACGCTGGGGTGC-ATG CACTTCGGTGTCGCCGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGTT AAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAA GCAACGCGCAGAACCTTACCAACCCTTGACATGTCCACtaTCGGCTCGAGAGATCGGGCT TTCAGTTcGGCTGGGTGGAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGA TGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTACCGCCAGTTGCCATCAT-TC-AGTT GGGCACTCTGGTGGAACTGCCGGTGACAAGCCGGAGGAAGGCGGGGATGACGTCAAGTCC TCATGGCCCTTATGGGTTGGGCTACACACGTGCTACAATGGCGGTGACAGTGGGATGCGA AGTCGCAAGATGGAGCCAATCCCC-AAAAGCCGTCTCAGTTCGGATTGCACTCTGCAACT CGGGTGCATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTT CCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGCTTTACCCGAAGGTGGTG CGCTAACCgGCAAcGGAGGCAGCCAACCACGGTCAGGTCAGCGACTGGGGTGAAGTCGTA ACAAGGTACCCGTAGGGGAACCTGCGGCTGGATCACCTCCTT-tctaaggaaaa >NC_016618:450802..452299 tgaac----CTGAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCATGCCTAACACA TGCAAGTCGAACGAAG-----GCTTCGGC------CTTAGTGGCGCACGGGTGAGTAACA CGTGGGA-ACCTGCCTTTCGGTTCGGGATAACGTCTGGAAACGGACGCTAACACCGGATA CG-------TCCTTCGGGA-------GAAAGTT-----TACGCCGAGAGAGGGGCCCGCG TCCGATTAGGTAGTTGGTGGGGTAATGGCCCACCAAGCCGACGATCGGTAGCTGGTCTGA GAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGT GGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGC CTTAGGGTTGTAAAGCTCTTTCGCACGCGACGATG-A-----------------TGACGG TAGCGTGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGC GAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCTGTTTAGTCAGAAGT GAAAGCCCCGGGCTTAACCTGGGAACGGCTTTTGATACTGGCAGGCTTGAGTTCCGGAGA GGATGGTGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTGGGAAGAACACCGGTGG CGAAGGCGGCCATCTGGACGGACACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAG GATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATGCTAGACGCTGGGGTGC-ATG CACTTCGGTGTCGCCGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGTT AAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAA GCAACGCGCAGAACCTTACCAACCCTTGACATGTCCACcaCCGGCTCGAGAGATCGGGCT TTCAGTTcGGCTGGGTGGAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGA TGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTACCGCCAGTTGCCATCAT-TC-AGTT GGGCACTCTGGTGGAACTGCCGGTGACAAGCCGGAGGAAGGCGGGGATGACGTCAAGTCC TCATGGCCCTTATGGGTTGGGCTACACACGTGCTACAATGGCGGTGACAGTGGGACGCGA AGTCGCAAGATGGAGCCAATCCCC-AAAAGCCGTCTCAGTTCGGATTGCACTCTGCAACT CGGGTGCATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTT CCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGCTTTACCCGAAGGTGGTG CGCTAACCcgGCAAgGGAGGCAGCCCACCACGGTCAGGTCAGCGACTGGGGTGAAGTCGT AACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCGCCTT-tttctaaagaa
Test files: