Augustus result interpretation

shashankgupta

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Join Date: Feb 2015

Posts: 35
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Augustus result interpretation

03-03-2015, 10:16 PM

Hi,

I am new to augutus and i used Augustus for fungal genome analysis.

i used command :

augustus --species=human --UTR=on sequence.fasta > sequence_augustus.gff

i got result

----- prediction on sequence number 1 (length = 11239, name = contig00001) -----
# Constraints/Hints:
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig00001 AUGUSTUS gene 1476 4367 1 + . g1
contig00001 AUGUSTUS transcript 1476 4367 . + . g1.t1
contig00001 AUGUSTUS tss 1476 1476 . + . transcript_id "g1.t1"; gene_id "g1";
contig00001 AUGUSTUS exon 1476 1559 . + . transcript_id "g1.t1"; gene_id "g1";
contig00001 AUGUSTUS exon 2030 4367 . + . transcript_id "g1.t1"; gene_id "g1";
contig00001 AUGUSTUS start_codon 2378 2380 . + 0 transcript_id "g1.t1"; gene_id "g1";
contig00001 AUGUSTUS CDS 2378 3223 . + 0 transcript_id "g1.t1"; gene_id "g1";
contig00001 AUGUSTUS stop_codon 3221 3223 . + 0 transcript_id "g1.t1"; gene_id "g1";
contig00001 AUGUSTUS tts 4367 4367 . + . transcript_id "g1.t1"; gene_id "g1";
# protein sequence = [MLDLEIAKNCADGELDGKMVEEHPGVDNKDGSHTDSKGGNKAKGEADWAGQAELPSHVTQTPIETELPLTIAPAIDAH
# TATEGVVSAAVVAANTRATASIGTSNALGNLSKLPEISRSLIYHFVTAETDFPCVNSECRPPRLLSTISKTIKKEVELYYRCNHRTLMVELNPFEFHH
# LEDSFPAWSLEEYRAYMAPYMKPVTSRVHDLSIVDEVIIHLADDGPDCLTLLYTLALDHTDPTIPGQSDHEPFRLTLEYASAEGDETRDMHNHEYCTR
# FRTFFEP]
# end gene g1

my question what above result indicates ? and what about protein sequence ? if this protein correspond to the first Nucleotide sequence (contig 1) in my complete fasta file (contains many contigs), should i use this protein sequence and do the BATCH CD search for annotation ? or any other tools for annotation for fungal genmone ?

Any suggestions.

Regards !

Shashank
Tags: seqencing, tools and techniques

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