Mercurial > repos > bgruening > augustus
view test-data/human_augustus_utr-on.gtf @ 9:bd0e53f3a891 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
| author | iuc |
|---|---|
| date | Fri, 04 Oct 2024 11:32:08 +0000 |
| parents | 09855551d713 |
| children |
line wrap: on
line source
# This output was generated with AUGUSTUS (version 3.4.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. # Looks like /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- # # Predicted genes for sequence number 1 on both strands # start gene HS04636.g1 HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1 HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag] # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] # end gene HS04636.g1 ### # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- # # Predicted genes for sequence number 2 on both strands # start gene HS08198.g2 HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2 HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 1772 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS tts 2105 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc # ggcgtggtga] # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF # HVLDGECTAGASMAAW] # end gene HS08198.g2 ### # command line: # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat --UTR=on --genemodel=complete --softmasking=0 --species=human