"Fossies" - the Fresh Open Source Software Archive

Member "augustus-3.3.3/docs/tutorial-cgp/data/augCGP_rnaseq/pred3/hg38.cgp.gff" (22 May 2019, 2018 Bytes) of package /linux/misc/augustus-3.3.3.tar.gz:


As a special service "Fossies" has tried to format the requested text file into HTML format (style: standard) with prefixed line numbers. Alternatively you can here view or download the uninterpreted source code file.

    1 # This output was generated with AUGUSTUS (version 3.3.1).
    2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
    3 # O. Keller, S. K├Ânig, L. Gerischer, L. Romoth and Katharina Hoff.
    4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
    5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
    7 #
    8 #----- prediction for species 'hg38' -----
    9 #
   10 #----- prediction on sequence range chr16:124001-170590 (46590bp) -----
   11 #
   12 # start gene g1
   13 chr16	AUGUSTUS	gene	127536	160062	0	-	.	g1
   14 chr16	AUGUSTUS	transcript	127536	160062	.	-	.	g1.t1
   15 chr16	AUGUSTUS	exon	127536	127720	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   16 chr16	AUGUSTUS	stop_codon	127576	127578	.	-	0	transcript_id "g1.t1"; gene_id "g1";
   17 chr16	AUGUSTUS	CDS	127576	127720	0.99	-	1	transcript_id "g1.t1"; gene_id "g1";
   18 chr16	AUGUSTUS	CDS	159185	160062	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
   19 chr16	AUGUSTUS	exon	159185	160062	.	-	.	transcript_id "g1.t1"; gene_id "g1";
   20 chr16	AUGUSTUS	start_codon	160060	160062	.	-	0	transcript_id "g1.t1"; gene_id "g1";
   21 # protein sequence = [MNIQEQGFPLDLGASFTEDAPRPPVPGEEGELVSTDPRPASYSFCSGKGVGIKGETSTATPRRSDLDLGYEPEGSASP
   22 # TPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKLEPCDSNEEKRLKLARAIYRKYILDNNGIVSRQTKPATKSFIKGCIMKQL
   23 # IDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTRTGSESPKVCSDQSSGSGTGKGISGYLPTLNEDEEWKCDQDMDEDDGRDAAPPGRLPQKLLLE
   24 # TAAPRVSSSRRYSEGREFRYGSWREPVNPYYVNAGYALAPATSANDSEQQSLSSDADTLSLTDSSV]
   25 # Evidence for and against this transcript:
   26 # % of transcript supported by hints (any source): 100
   27 # CDS exons: 2/2
   28 #      W:   2 
   29 # CDS introns: 1/1
   30 #      E:   1 
   31 # 5'UTR exons and introns: 0/0
   32 # 3'UTR exons and introns: 1/1
   33 #      W:   1 
   34 # hint groups fully obeyed: 51
   35 #      E:   1 
   36 #     RM:  36 
   37 #      W:  14 
   38 # incompatible hint groups: 103
   39 #      E:   1 
   40 #      W: 102 
   41 # end gene g1
   42 ###
   43 #----- prediction on sequence range chr16:168617-176000 (7384bp) -----
   44 #
   45 # (none)