[maker-devel] maker exon result
Carson Holt
carsonhh at gmail.com
Fri Jun 21 07:58:35 MDT 2013
To further illustrate this I've highlighted the location of all CDS entries.
You need to cut them out, string them together linearly, and only then can
you translate. There is a start codon for the merged CDS then all open
reading frame following that, but no stop codon so this is a partial
transcript. Sometimes the gene predictors do not find a likely stop and a
partial model scores better. You can force MAKER to try and find a stop
even when the gene predictor (snap, augustus, etc.) doesn't by setting
always_complete=1 in the maker_opts.ctl file. Keep in mind that this is just
a forced canonical completion.
ATGAAGGGCGCGATACGTACTACGATTCCAAAACCATCAGCATTGCCATTGAAGGTCTCA
GAATTATCTCCATCAGCTGATTCAGTACCCGTTCCAGCGTCTTTACAGGATGTCGAGGCG
GGGAAGTTGATTGAGAATAATCCATCAGGGgtgatacagaagaattgtttcagTATCTTG
TTGAAATATTGGCTTCTAGAGTGTATGATGTAGCAATTGATTCCCCCTTGCAAAATGCAA
CTAAGCTTTCCAAGAAGCTTGGAGTTAACTTTTGGATCAAAAGAGAGGATATGCAGTCCg
tatgtttctcctctcttctttttttgatgtagcatttgctttaacttagaatttgtggtt
ttaaacataccattagaaaggtatggaggttgaggattagggtagtaaagtaggtagtct
agagtgttcataacagtaatattgacaagcagtctcgctttccgttggtagtaggttttt
atgactaaccgttattttctttcattgttgatcaacttacttttgttgtttttattctgc
ttttatatggctttttggtactgtcccttcttgtctatattttcattaatgtggtgctta
tgcttttctaagccgagagtttattggaaacaactttcatatcctcacaaggtaggggta
aggtgtgcgtacacactaccctccccagactctacggtgtgggataatatttagtatgtt
attgtcgttgttgttgtaaacgttttttttgttgctatcaaagcatgttattacgggtaa
aatagaaacatttaaagtgaaagagtttccaaacgtaggaaagcttttttttctttcgga
atacaccgaaaaaagaaagactatcatttaagatagaacaacaacagcgacggagctagc
cttcgacttactggttcggcagaacccaataattttggcccaaactctgtacttgtacta
aaaagctcacttaatatgtataaaaagcctagtaattaagttgcatttttttctttctaa
aatctagagctcataaactcaaaattatgtctccgcctctgaacaatggggatattattc
tacttttaactatcttagataagttaataattgttctctttttcaaacgtttctgccttg
tattattgtgtaactatttatactgtgtggacgcttcaaaatgttgttgcgcccgcgtcg
gatcctcaaaaaatatatattttgaggattcgacacgcacccgatgaccttttcggagaa
ttcgagcaatataggtaactaatattgctagctcatcaactggtggtattttttagGTGC
TCTCATTCAAGCTTAGAGGAGCTTATAACATGATGACCAAACTCTCAAAGGAGCAATTAG
AAAGAGGGGTTATAACTGCTTCAGCTGGAAATCATGCACAAGGTGTTGCATTAGGTGCTC
AGAGACTTAAATGTACTGCTACGATTgtcatgcctgttaccacaccagagatcaaggtaa
ttagttctctcctgttaatttatccttcatgttcgattcatgtgaatctagttgatcggg
cactgagttttactaaaaaatgaagactttcggaacttgggagctttaacatgctgtaac
atttgtgtagttataagacttttgaaacttatagtcttagtgggtgtttggacataagaa
ttgtaaagttccaagaaaagtgaaaaaaaattcaagtgaaaatggtatttgaaaattaga
gttgtgtttggacatgaatataattttaggttgtttttgaagttttgtgagtgatctgac
acaaattttgaaaaaacaactttttggagtttttcaaattttcgaaaaattccaaaatgc
atcttcaagtgaaaattggaaattatatgaccaaacgctgatttcgggaaaaaaattcga
aaaaatgtgaaaattttcttatgtccaaacgggctcttaaatgcgtcataacgtttgtgt
ggttataaaagtctctcatctgaatagggtcacacaactaaaacagagagaacaaaataa
ttcactaaaaaaaaattggaactagctacaaacttcgtcgcaagtctcgctaaatcgctc
gtagctaatagaatttctagataatttgtttagcttgtagcatgaaatttttctatttag
caacagaagtagtctgtcgctaattcctatttttttagtagaaagtattgtgaaattatt
tgtttttctaaaggaccattttctttacaaatgaacagattgaagcagttaagaacttgg
atggtaatgtagttctacagGGTGACACATTTGATGAAGCTCAAGCACATGCTTTAAAGT
TGGCTGAAGATGAAGgtctcacattcatcccgcctttcgatcacatcttaaagatataca
tgcagtatttctgcctgtagGAGGAGGAGGTTTAATAGCTGGTGTTGCTGCATATTTCAA
AAGGGTTGCTCCTCATACAAAGATTATAGGAGTTGAGCCATTTGGTGCAAGTTCAATGAC
ACAGTCTTTGTACCACGGAATGAGAGTAAAGTTAGAACAAGTTGATAATTTTGCAGATGG
CgtagctgttgcactagTTAGTTGGTGAAGAAACTTTCCGTCTTTGCAAAGATTTAATAG
ACGGAATGGTCTTAGTCAGTAACGATGCTATTAGTGCAGCAGTAAAGgttagcacgcacc
atctcctaatggtttcagatatgatccgtccaaccagccaaaattggttagaataggacg
ggttgaactatcaacccaatcaatcacagcccaaataacatttatgtgggtatatgactc
gcccatttattaactcaaccaattttggtccattcaaattcaggctaacccgtccacgtt
tgacattcatactttagatgtggattaaagtaactttcttaaatttccctctggttttga
catgtactagtttgtgtttgtgtgtgttttgttctttttttcaatagGATGTGTACGACA
AAGGAAGGAACATATTAGAGACATCAGGTGCACTCGCCATAGCTGGAGCTGAAGCATACT
GCAAATACTATGACATAAAGGGCGAAAACGTTGTAGCAATTGCTAGTGGAGCCAATATGG
ACATCAGCAAACTAAAATTAGTCGTCGATTTAGCAGATATTGGTGGACAGAGGGAAGCTC
TGCTGGCTACTTTTATGCCAGAAGAACCAGGAAGCTTCAAAAAATTCTGCGAACTTgtgc
gttacttagagcacttaacaagcattttagccagagtttaagttatatacatcgtcgtca
gtgtaagaaacttttataccgtcttgatggagtaaaaatttgttacactgacgtgtacat
aacttaaaacttttttagttactatatgatactttctgtctaagaaactgaaatattgac
ttgaattactggtgggacctatgattattaccgaattcaagtacagatataactctggaa
gaaaacaagctctagttctgtacaggtaattaaagttctattcatttttagaggggatgt
tggcttctcattttagatttgctttattagttgttaggaaaaaagaaattacttattaca
ttcaatttttagATTTTCTGTCAATTCATATTTCCTGAGAAGCCTGGAGCTTTAAGGAAG
TTCTTAGATGCTTTCAGCCCTCGATGGAATATAAGTTTGTTCCATTATCGTGAACAG
Thanks,
Carson
From: Barry Moore <bmoore at genetics.utah.edu>
Date: Thursday, 20 June, 2013 9:29 PM
To: Jingjing Jin <jjin01 at mail.rockefeller.edu>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker exon result
To clarify things a bit Jin. Not every exon will have a start and/or stop
codon only the fist coding exon will have a start and the last coding exon
will have a stop. In the GFF3 format a coding exon is a feature of type
'CDS' (column 3) so only look at CDS features not at 'exon' features. For
CDSs you must then concatenate the sequence I'd each CDS line for a given
transcript (and reverse compliment the sequence if it is on the minus
strand). The resulting sequence will usually (but not always) have start and
stop codons at the beginning and end.
B
Barry Moore
Research Scientist
Dept. Human Genetics
University of Utah
On Jun 20, 2013, at 6:18 PM, "Jingjing Jin" <jjin01 at mail.rockefeller.edu>
wrote:
> For my understanding, the prediction gene model should be connect different
> exon together.
>
> For each exon of a gene, I think it should have a start codon and stop codon.
> However, it may be wrong.
>
> However, when I check some gene model from maker prediction, some exon of one
> gene, I cannot find stop codon for it. Like the example I give, the red color
> is the first exon. However, the last 3 NT is not a stop codon.
>
> Even for last 3 NT for last exon, it is also not a stop codon.
>
> Is it reasonable?
>
> Thanks!
>
> Jingjing
>
>
>
> From: Daniel Ence [dence at genetics.utah.edu]
> Sent: Thursday, June 20, 2013 7:06 PM
> To: Jingjing Jin; maker-devel at yandell-lab.org
> Subject: RE: maker exon result
>
> Hi Jingjing,
>
> It's really hard to find the stop codon in the nucleotide sequence that you
> sent. I think most people determine the presence of a stop codon in a gene by
> viewing the annotations and sequence in some kind of viewer. The one that I
> use the most is Apollo, but many people also like gbrowse and igv.
>
> When you view gene models in Apollo, the start codons are highlighted in green
> and the stop codons are highlighted in red. Sometimes MAKER couldn't find the
> stop or start codon for a gene, and in those cases, the end of the gene model
> is marked with an orange arrow.
>
> I hope that I understood your question. Feel free to reply back on the mailing
> list if I didn't.
>
> Thanks,
> Daniel
>
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Jingjing
> Jin [jjin01 at mail.rockefeller.edu]
> Sent: Thursday, June 20, 2013 2:22 PM
> To: maker-devel at yandell-lab.org
> Subject: [maker-devel] maker exon result
>
> Dear all,
>
> I have used maker to predict the gene model in my draft genome.
>
> However, when I check the sequence for each exon, I find some of them just
> have start codon, without stop codon.
>
> Is it reasonable for this?
>
> Like in this example:
>
> processed_tobacco_genome_sequences_c33 maker gene 8916 12632 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9;Name=maker-proce
> ssed_tobacco_genome_sequences_c33-snap-gene-0.9
> processed_tobacco_genome_sequences_c33 maker mRNA 8916 12632 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1;Parent=ma
> ker-processed_tobacco_genome_sequences_c33-snap-gene-0.9;Name=maker-processed_
> tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0
> |0|1|0.14|0.12|8|0|362
> processed_tobacco_genome_sequences_c33 maker exon 8916 9065 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:148;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker exon 9089 9214 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:149;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker exon 10232 10381 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:150;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker exon 11216 11270 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:151;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker exon 11336 11496 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:152;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker exon 11513 11602 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:153;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker exon 11903 12151 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:154;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker exon 12528 12632 .
> + .
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:155;
> Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 8916 9065 .
> + 0
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 9089 9214 .
> + 0
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 10232 10381 .
> + 0
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 11216 11270 .
> + 0
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 11336 11496 .
> + 2
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 11513 11602 .
> + 0
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 11903 12151 .
> + 0
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
> processed_tobacco_genome_sequences_c33 maker CDS 12528 12632 .
> + 0
> ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Paren
> t=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
>
>
> ATGAAGGGCGCGATACGTACTACGATTCCAAAACCATCAGCATTGCCATTGAAGGTCTCAGAATTATCT
> CCATCAGCTGATTCAGTACCCGTTCCAGCGTCTTTACAGGATGTCGAGGCGGGGAAGTTGATTGAGAAT
> AATCCATCAGGGGTGATACAGAAGAATTGTTTCAGTATCTTGTTGAAATATTGGCTTCTAGAGTGTATG
> ATGTAGCAATTGATTCCCCCTTGCAAAATGCAACTAAGCTTTCCAAGAAGCTTGGAGTTAACTTTTGGA
> TCAAAAGAGAGGATATGCAGTCCGTATGTTTCTCCTCTCTTCTTTTTTTGATGTAGCATTTGCTTTAAC
> TTAGAATTTGTGGTTTTAAACATACCATTAGAAAGGTATGGAGGTTGAGGATTAGGGTAGTAAAGTAGG
> TAGTCTAGAGTGTTCATAACAGTAATATTGACAAGCAGTCTCGCTTTCCGTTGGTAGTAGGTTTTTATG
> ACTAACCGTTATTTTCTTTCATTGTTGATCAACTTACTTTTGTTGTTTTTATTCTGCTTTTATATGGCT
> TTTTGGTACTGTCCCTTCTTGTCTATATTTTCATTAATGTGGTGCTTATGCTTTTCTAAGCCGAGAGTT
> TATTGGAAACAACTTTCATATCCTCACAAGGTAGGGGTAAGGTGTGCGTACACACTACCCTCCCCAGAC
> TCTACGGTGTGGGATAATATTTAGTATGTTATTGTCGTTGTTGTTGTAAACGTTTTTTTTGTTGCTATC
> AAAGCATGTTATTACGGGTAAAATAGAAACATTTAAAGTGAAAGAGTTTCCAAACGTAGGAAAGCTTTT
> TTTTCTTTCGGAATACACCGAAAAAAGAAAGACTATCATTTAAGATAGAACAACAACAGCGACGGAGCT
> AGCCTTCGACTTACTGGTTCGGCAGAACCCAATAATTTTGGCCCAAACTCTGTACTTGTACTAAAAAGC
> TCACTTAATATGTATAAAAAGCCTAGTAATTAAGTTGCATTTTTTTCTTTCTAAAATCTAGAGCTCATA
> AACTCAAAATTATGTCTCCGCCTCTGAACAATGGGGATATTATTCTACTTTTAACTATCTTAGATAAGT
> TAATAATTGTTCTCTTTTTCAAACGTTTCTGCCTTGTATTATTGTGTAACTATTTATACTGTGTGGACG
> CTTCAAAATGTTGTTGCGCCCGCGTCGGATCCTCAAAAAATATATATTTTGAGGATTCGACACGCACCC
> GATGACCTTTTCGGAGAATTCGAGCAATATAGGTAACTAATATTGCTAGCTCATCAACTGGTGGTATTT
> TTTAGGTGCTCTCATTCAAGCTTAGAGGAGCTTATAACATGATGACCAAACTCTCAAAGGAGCAATTAG
> AAAGAGGGGTTATAACTGCTTCAGCTGGAAATCATGCACAAGGTGTTGCATTAGGTGCTCAGAGACTTA
> AATGTACTGCTACGATTGTCATGCCTGTTACCACACCAGAGATCAAGGTAATTAGTTCTCTCCTGTTAA
> TTTATCCTTCATGTTCGATTCATGTGAATCTAGTTGATCGGGCACTGAGTTTTACTAAAAAATGAAGAC
> TTTCGGAACTTGGGAGCTTTAACATGCTGTAACATTTGTGTAGTTATAAGACTTTTGAAACTTATAGTC
> TTAGTGGGTGTTTGGACATAAGAATTGTAAAGTTCCAAGAAAAGTGAAAAAAAATTCAAGTGAAAATGG
> TATTTGAAAATTAGAGTTGTGTTTGGACATGAATATAATTTTAGGTTGTTTTTGAAGTTTTGTGAGTGA
> TCTGACACAAATTTTGAAAAAACAACTTTTTGGAGTTTTTCAAATTTTCGAAAAATTCCAAAATGCATC
> TTCAAGTGAAAATTGGAAATTATATGACCAAACGCTGATTTCGGGAAAAAAATTCGAAAAAATGTGAAA
> ATTTTCTTATGTCCAAACGGGCTCTTAAATGCGTCATAACGTTTGTGTGGTTATAAAAGTCTCTCATCT
> GAATAGGGTCACACAACTAAAACAGAGAGAACAAAATAATTCACTAAAAAAAAATTGGAACTAGCTACA
> AACTTCGTCGCAAGTCTCGCTAAATCGCTCGTAGCTAATAGAATTTCTAGATAATTTGTTTAGCTTGTA
> GCATGAAATTTTTCTATTTAGCAACAGAAGTAGTCTGTCGCTAATTCCTATTTTTTTAGTAGAAAGTAT
> TGTGAAATTATTTGTTTTTCTAAAGGACCATTTTCTTTACAAATGAACAGATTGAAGCAGTTAAGAACT
> TGGATGGTAATGTAGTTCTACAGGGTGACACATTTGATGAAGCTCAAGCACATGCTTTAAAGTTGGCTG
> AAGATGAAGGTCTCACATTCATCCCGCCTTTCGATCACATCTTAAAGATATACATGCAGTATTTCTGCC
> TGTAGGAGGAGGAGGTTTAATAGCTGGTGTTGCTGCATATTTCAAAAGGGTTGCTCCTCATACAAAGAT
> TATAGGAGTTGAGCCATTTGGTGCAAGTTCAATGACACAGTCTTTGTACCACGGAATGAGAGTAAAGTT
> AGAACAAGTTGATAATTTTGCAGATGGCGTAGCTGTTGCACTAGTTAGTTGGTGAAGAAACTTTCCGTC
> TTTGCAAAGATTTAATAGACGGAATGGTCTTAGTCAGTAACGATGCTATTAGTGCAGCAGTAAAGGTTA
> GCACGCACCATCTCCTAATGGTTTCAGATATGATCCGTCCAACCAGCCAAAATTGGTTAGAATAGGACG
> GGTTGAACTATCAACCCAATCAATCACAGCCCAAATAACATTTATGTGGGTATATGACTCGCCCATTTA
> TTAACTCAACCAATTTTGGTCCATTCAAATTCAGGCTAACCCGTCCACGTTTGACATTCATACTTTAGA
> TGTGGATTAAAGTAACTTTCTTAAATTTCCCTCTGGTTTTGACATGTACTAGTTTGTGTTTGTGTGTGT
> TTTGTTCTTTTTTTCAATAGGATGTGTACGACAAAGGAAGGAACATATTAGAGACATCAGGTGCACTCG
> CCATAGCTGGAGCTGAAGCATACTGCAAATACTATGACATAAAGGGCGAAAACGTTGTAGCAATTGCTA
> GTGGAGCCAATATGGACATCAGCAAACTAAAATTAGTCGTCGATTTAGCAGATATTGGTGGACAGAGGG
> AAGCTCTGCTGGCTACTTTTATGCCAGAAGAACCAGGAAGCTTCAAAAAATTCTGCGAACTTGTGCGTT
> ACTTAGAGCACTTAACAAGCATTTTAGCCAGAGTTTAAGTTATATACATCGTCGTCAGTGTAAGAAACT
> TTTATACCGTCTTGATGGAGTAAAAATTTGTTACACTGACGTGTACATAACTTAAAACTTTTTTAGTTA
> CTATATGATACTTTCTGTCTAAGAAACTGAAATATTGACTTGAATTACTGGTGGGACCTATGATTATTA
> CCGAATTCAAGTACAGATATAACTCTGGAAGAAAACAAGCTCTAGTTCTGTACAGGTAATTAAAGTTCT
> ATTCATTTTTAGAGGGGATGTTGGCTTCTCATTTTAGATTTGCTTTATTAGTTGTTAGGAAAAAAGAAA
> TTACTTATTACATTCAATTTTTAGATTTTCTGTCAATTCATATTTCCTGAGAAGCCTGGAGCTTTAAGG
> AAGTTCTTAGATGCTTTCAGCCCTCGATGGAATATAAGTTTGTTCCATTATCGTGAACAG
>
>
>
>
> This is the sequence for this gene, the red color is for the first exon??
>
>
> However, for this exon, I cannot found the stop codon???
>
>
> I also find for some exon, there are several stop codon in one exon???
>
>
> Does anyone have the same problem with me?
>
> Or there is something wrong when I configure the maker file??
>
>
> Thanks!
>
>
> Jingjing
>
>
>
>
>
> _______________________________________________
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