augustus-gene-calls [artifact]

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Description

TXT

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

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There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required or used by

anvi-script-augustus-output-to-external-gene-calls

Description

A gene call file from AUGUSTUS.

AUGUSTUS is a tool to predict genes from a variety of Eurkaryotic genomes. This includes predicting the 5’ UTR and 3’ UTR, as well as introns. You can search a sequence in the Augustus web interface. After a search, you can export the results as a .gff text file.

As of now, Anvi’o (specifically anvi-script-augustus-output-to-external-gene-calls) is only tested with AUGUSTUS v3.3.3. Feel free to be adventurous and try other versions if you feel so inclined.

You can convert this file into an anvi’o external-gene-calls file using anvi-script-augustus-output-to-external-gene-calls.

Here is an example of a .gff file for the Homo sapiens RNAP III subunit D sequence:

# This output was generated with AUGUSTUS (version 3.3.3).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. KÃ¶nig, 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 /data/www/augustus/augustus/config/ ...
# human version. Using default transition matrix.
# Looks like /data/www/augustus/webservice/data/AUG-707407769/input.fa 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 = 5336, name = unnamed-1) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
unnamed-1    AUGUSTUS    gene    57    1253    1    +    .    g1
unnamed-1    AUGUSTUS    transcript    57    1253    1    +    .    g1.t1
unnamed-1    AUGUSTUS    start_codon    57    59    .    +    0    transcript_id "g1.t1"; gene_id "g1";
unnamed-1    AUGUSTUS    single    57    1253    1    +    0    transcript_id "g1.t1"; gene_id "g1";
unnamed-1    AUGUSTUS    CDS    57    1253    1    +    0    transcript_id "g1.t1"; gene_id "g1";
unnamed-1    AUGUSTUS    stop_codon    1251    1253    .    +    0    transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcggaaggaaacgccgccggcgagcccagcacgccgggagggccccgacctctcctgactggggcccgggggctca
# tcgggcggcggccggcgcctcccctcacccccggccgccttccctccatccgttccagggacctcaccctcgggggagtcaagaagaaaaccttcacc
# ccaaatatcatcagtcggaagatcaaggaagagcccaaggaagaagtaactgtcaagaaggagaagcgtgaaagggacagagaccgacaacgagaggg
# gcatggacgagggcgaggccgtccagaagtgatccagtctcactccatctttgagcagggcccagctgaaatgatgaagaaaaaagggaactgggata
# agacagtggatgtgtcagacatgggaccttctcatatcatcaacatcaaaaaagagaagagagagacagacgaagaaactaaacagatcttgcgtatg
# ctggagaaggacgatttcctcgatgaccccggcctgaggaacgacactcgaaatatgcctgtgcagctgccgctggctcactcaggatggctttttaa
# ggaagaaaatgacgaaccagatgttaaaccttggctggctggccccaaggaagaggacatggaggtggacatacctgctgtgaaagtgaaagaggagc
# cacgagatgaggaggaagaggccaagatgaaggctcctcccaaagcagccaggaagactccaggcctcccgaaggatgtatctgtggcagagctgctg
# agggagctgagcctcaccaaggaagaggaactgctgtttctgcagctgccagacaccctccctggccagccacccacccaggacatcaagcctatcaa
# gacagaggtgcagggcgaggacggacaggtggtgctcatcaagcaggagaaagaccgagaagccaaattggcagagaatgcttgtaccctggctgacc
# tgacagagggtcaggttggcaagctactcatccgcaagtctggaagggtgcaactcctcttgggcaaggtgactctggacgtgaccatgggaactgcc
# tgctccttcctgcaggagctggtgtccgtgggccttggagacagtaggacaggggagatgacagtcctgggacacgtgaagcacaaacttgtatgttc
# ccctgattttgaatccctcttggatcacaaacaccggtaa]
# protein sequence = [MSEGNAAGEPSTPGGPRPLLTGARGLIGRRPAPPLTPGRLPSIRSRDLTLGGVKKKTFTPNIISRKIKEEPKEEVTVK
# KEKRERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKGNWDKTVDVSDMGPSHIINIKKEKRETDEETKQILRMLEKDDFLDDPGLRNDTRNM
# PVQLPLAHSGWLFKEENDEPDVKPWLAGPKEEDMEVDIPAVKVKEEPRDEEEEAKMKAPPKAARKTPGLPKDVSVAELLRELSLTKEEELLFLQLPDT
# LPGQPPTQDIKPIKTEVQGEDGQVVLIKQEKDREAKLAENACTLADLTEGQVGKLLIRKSGRVQLLLGKVTLDVTMGTACSFLQELVSVGLGDSRTGE
# MTVLGHVKHKLVCSPDFESLLDHKHR]
# end gene g1
###
# command line:
# /data/www/augustus/augustus/bin/augustus --species=human --strand=both --singlestrand=false --genemodel=partial --codingseq=on --sample=100 --keep_viterbi=true --alternatives-from-sampling=true --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=2 /data/www/augustus/webservice/data/AUG-707407769/input.fa --exonnames=on

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