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hyattpd / Prodigal

Prodigal Gene Prediction Software
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Predicted CDSs of plasmid AF149757.1 have interior stop codons #86

Open vbrover opened 3 years ago

vbrover commented 3 years ago 
$ prodigal  -i AF149757.1  -d out  -p meta
-------------------------------------
PRODIGAL v2.6.3 [February, 2016]         
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.     
-------------------------------------
Request:  Metagenomic, Phase:  Training
Initializing training files...done!
-------------------------------------
Request:  Metagenomic, Phase:  Gene Finding
Finding genes in sequence #1 (6886 bp)...done!
DEFINITION  seqnum=1;seqlen=6886;seqhdr="AF149757.1";version=Prodigal.v2.6.3;run_type=Metagenomic;model="1|Mycoplasma_pneumoniae_M129|B|40.0|4|0";gc_cont=40.00;transl_table=4;uses_sd=0
FEATURES             Location/Qualifiers
     CDS             500..1012
                     /note="ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.491;conf=92.12;score=10.70;cscore=7.03;sscore=3.67;rscore=0.02;uscore=-1.75;tscore=5.40;"
     CDS             complement(1256..1552)
                     /note="ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.404;conf=92.36;score=10.84;cscore=8.67;sscore=2.17;rscore=0.02;uscore=-2.59;tscore=5.40;"
     CDS             3184..3531
                     /note="ID=1_3;partial=00;start_type=ATG;rbs_motif=AAAAA;rbs_spacer=15bp;gc_cont=0.443;conf=98.65;score=18.67;cscore=10.78;sscore=7.89;rscore=2.94;uscore=-0.46;tscore=5.40;"
     CDS             3755..4258
                     /note="ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.444;conf=99.51;score=23.08;cscore=20.28;sscore=2.80;rscore=0.02;uscore=-1.96;tscore=5.40;"
     CDS             4584..4796
                     /note="ID=1_5;partial=00;start_type=ATG;rbs_motif=AAAAAA;rbs_spacer=13bp;gc_cont=0.423;conf=99.93;score=31.48;cscore=18.32;sscore=13.16;rscore=5.49;uscore=3.79;tscore=4.53;"
     CDS             complement(5342..6160)
                     /note="ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.454;conf=100.00;score=57.10;cscore=49.85;sscore=7.25;rscore=0.02;uscore=0.54;tscore=5.40;"
//

Predicted CDSs:

$ cat out
>AF149757.1_1 # 500 # 1012 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.491
ATGAGGGATAAGAAGCTCTCCTTATGTGCCAAAAGGGCGGTAAACGCTACGCTAGTCACCGTAAGGAAAT
CAACGCTCTTACACCTACAGACCTTGCTCAGCAGGGATTTGTTCTCTGTATCACACGATACACAAAGTGA
CACACCGCAACTACCAAGCTATGCCGAGCTTTGTAATGAGATCAAAGAGCTGAGACATAGCGTTACGTCA
CTCACCTCCGCACTTATCGAAATATGTGACAAGGTAACACGTAACGTTACGCCCCAAACCGCACCTAAGC
CTCAGCAGAAACGTTCAGTGAGCGACAATGAGCGCCGAGCCGCCGAGGCTCAAGCCAAGGTTTTCAAGGT
GTTGGAGCGATATAAGGGCAAAGACAATAAGCCATCAATCCGAGCGATGGCAGAGGAAGCCGGAGTACAC
AACACCACTTTTTCTAGGCACAAGAAAACTTGGGAGGCACAAAGTGACGTATCAGTTGTAACGATTCATC
GTGTCGCCCCTGCAAACACGTAG
>AF149757.1_2 # 1256 # 1552 # -1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.404
ATGAAGATCCCTGATGATAAAATTCAGCAACACAGTGTCNCCAAAGAGGAACAANTACAGTATATAGAGA
CAGTAAAAAGATCAGGGAGGAAGAGAATAAGCAAAGGTTGGATGACACTCTTCCGATGCTATGCCTATCT
ATGAGTAGGAGCCATTAAAACACTAGAAGGCATTACAAGTGGCATAGCAATAGCCGACATCGAAAAGACA
GAAGAGCTTGTGGAGAAACTCAAGCAAGAACTAGTCGACACAAGAAGAATGCAAAAAAAAGAAATTGACA
AAACGGCGCCTAATTAA
>AF149757.1_3 # 3184 # 3531 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=AAAAA;rbs_spacer=15bp;gc_cont=0.443
ATGAGCAAGAGCGACAAAAACAAGCGCACGAAGGTGATACAACTTCGTGTATCGGAAGAAGAAAAAGCCA
TCATGCAGAAGCATGCCAATGGCAACGTTTCAGACTGGCTCAGAGCCTACGGTCTGAATCCAAAAAACCC
ACACCATAAACCTCAGTATCGAGAGCTAAAGCAAGATCCTGAAGTGGTGCGTCAATTGGCGTTTATTGGC
AATAACGTAAACCAAATCGCCCGAAAAATTAACACCATCGATAAATCTGAGGGTGCATTAAATCTAGTCT
CATTACAGGCTCAGTTACTACAGGCCAACGAGCTACTAGAGCAAATCGCAAAACCACAACGATGATAG
>AF149757.1_4 # 3755 # 4258 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.444
ATGAGGCTGTTTGAGGAAACGTTGATGGTTGGTTTAGATCCAGACCAGTACGACATTGTCTGGATTGAGC
ATCGAGACAAAGACCGTCTGGAATTGAATTTTCACATCGTGAATATGGAACTCAGCACTGGCAAGGCGCT
AACGCCTTACGTGCATAGTCGAGACGTGAAACGTATCGATACATGGAAGTGTATCATCAATGACCATTAC
GGTTTCAGCGACCCAAACGACCCGTCTCACCAGCGTACCTTTACGTTTGGCAACAACAACCAAACGAGAC
AAGACATCATGAAACAGATTGATACGTATCTGTTTCAGCTTGCTGGAGACGGCGAACTTAACTCTCAAGA
TGATGTTAAAAACGCACTGGATGCCATCAATGGTGTATCGGTGACACGTACCACTAAGTCGTCCATCTCA
ATCAAGGTCGATGGGCAAGAAAAAGCAATAAGAATGAAAGGTGAAATGTATGGCAAACGGTTATGGAGGA
ATTGAAAACCTTAG
>AF149757.1_5 # 4584 # 4796 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=AAAAAA;rbs_spacer=13bp;gc_cont=0.423
ATGTTAAGCACAGTCCTAGACAACCTCAAAAACCTGCAAAATGGGTGGTCGAAATCCTCGCAAAAATTAG
AGAAGCAGTTACAAGAGTTACAGAAAGAGTTACAGAGCGAAAAGCAGAAGCGTCAGAGCTTGGAAAAGAG
TATCAGCGAACTCAACAAAACTGTATCGAGCTTGATCGATTACTTAAAGGCGGAAAGTACGGGCCAGCAA
TAA
>AF149757.1_6 # 5342 # 6160 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.454
ATGGTCCGTGAAGCTAACGACTTACGCCACATACCGTATCGATATCGAAGAATCTCTGCCGTATGGGGGC
TTAAGAAGTCCAACTCAGTGAGTGATCAGCTCAATGTTGCAATTGGTTATGATGAGTCGACTCAGCTAGC
GAACATCATGAATTTGTGCTTTAAACACAAAGCAAAGAACTCAAGCAAGGTTGAGTATATTAATGTGATT
AGCAAAGCATCAGTGGAAGAAGGGGTGCTCTCTGTTCGGTTTACAGACGACATCCTGCCGTATTTAATCA
ACCTATCTTCGTATACCACAATTCCTTTTAAAGCCACCGTTGGCTTTAACTGCAATTACTCATTTGCGAT
GCTGGAGCACCTACTGAAGCGTTACACAAAAGGGGGAGACTACCCTAGCCACGACATTCCACTGGCGGAC
TTGCATCAAATCTTAGGTACAAACACAGTTAAGAGCTATCAAGTGTGGAGTAGTTTTAAGAAGCGTGCTC
TGGATGCTATCGAGAAAGATTTTTCATTGATTGCTGGCGGCGGCTATGAGATTAGCTTTGAGCCTGTCTA
TGCCAAGGCCAAAGGGCGTGGTAGGCGTAGTGTTGAGGCTGTTACAGTGAACTTCACAAATGATGGTCTG
AAGCGCTTCCAGAGTGCCGTAAGCGCCAAGAAGGCTGGGCTGGATTACTTTATCGAAAACAACGATGAGG
CACTTTTACCAAACAATACCGCTGAGGAAGTTCGCCAAAAGCGAGCAGAACTGAGCAACAAGAAGCCAAA
ACCAAAATGCCCAGAGCCGAAGGTTGTTGAGGATGACTTCCTCTTCTAA

Translation:

>AF149757.1_1 # 500 # 1012 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.491
MRDKKLSLCAKRAVNATLVTVRKSTLLHLQTLLSRDLFSVSHDTQSDTPQLPSYAELCNEIKELRHSVTSLTSALIEICD
KVTRNVTPQTAPKPQQKRSVSDNERRAAEAQAKVFKVLERYKGKDNKPSIRAMAEEAGVHNTTFSRHKKTWEAQSDVSVV
TIHRVAPANT*
>AF149757.1_2 # 1256 # 1552 # -1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.404
MKIPDDKIQQHSVXKEEQXQYIETVKRSGRKRISKGWMTLFRCYAYL*VGAIKTLEGITSGIAIADIEKTEELVEKLKQE
LVDTRRMQKKEIDKTAPN*
>AF149757.1_3 # 3184 # 3531 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=AAAAA;rbs_spacer=15bp;gc_cont=0.443
MSKSDKNKRTKVIQLRVSEEEKAIMQKHANGNVSDWLRAYGLNPKNPHHKPQYRELKQDPEVVRQLAFIGNNVNQIARKI
NTIDKSEGALNLVSLQAQLLQANELLEQIAKPQR**
>AF149757.1_4 # 3755 # 4258 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.444
MRLFEETLMVGLDPDQYDIVWIEHRDKDRLELNFHIVNMELSTGKALTPYVHSRDVKRIDTWKCIINDHYGFSDPNDPSH
QRTFTFGNNNQTRQDIMKQIDTYLFQLAGDGELNSQDDVKNALDAINGVSVTRTTKSSISIKVDGQEKAIRMKGEMYGKR
LWRN*KP*
>AF149757.1_5 # 4584 # 4796 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=AAAAAA;rbs_spacer=13bp;gc_cont=0.423
MLSTVLDNLKNLQNGWSKSSQKLEKQLQELQKELQSEKQKRQSLEKSISELNKTVSSLIDYLKAESTGQQ*
>AF149757.1_6 # 5342 # 6160 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.454
MVREANDLRHIPYRYRRISAVWGLKKSNSVSDQLNVAIGYDESTQLANIMNLCFKHKAKNSSKVEYINVISKASVEEGVL
SVRFTDDILPYLINLSSYTTIPFKATVGFNCNYSFAMLEHLLKRYTKGGDYPSHDIPLADLHQILGTNTVKSYQVWSSFK
KRALDAIEKDFSLIAGGGYEISFEPVYAKAKGRGRRSVEAVTVNFTNDGLKRFQSAVSAKKAGLDYFIENNDEALLPNNT
AEEVRQKRAELSNKKPKPKCPEPKVVEDDFLF*

CDSs AF149757.1_3 and AF149757.1_4 have interior stop codons.