 Search Parameters
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User Name
Put your name or id.
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Mapping Title
Put title for the search. It will be printed at the top of result page. If the title is left blank, it will be named automatically.
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Mapping Environment (this option is applied all kinds of mapping)
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Peptide List
Put a peptide list file. This format is followed below.
DFKLSDEETATILSFNR
ISLSPEYVFSVSTFQELPSLEQK
TLVTLPLLFLLPK
FISGHTSELGNFR
FQTIDIEPDIEALLSQGLSCA
GETGPAGPPGAPGAPGAPGPVGPAGKSGDRGETGPAGPAGPVGPVGAR
IIEDLGVHFLQYVLK
KDEGEGAAGAGDHQDPSLGAGEAASK
AAECSDFPVPSTEGTPIQGSK
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Supported mapping methods
PV: Mapping protein database first to filter out known peptides, and then mapping variant splice graph.
PS: Mapping protein database first to filter out known peptides, and then mapping six-frame translation database.
VO: Mapping variant splice graph only.
VO: Mapping six-frame translation database only.
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Isoleucine is equivalent to leucine
Identified peptides from tandem mass spectrometry do not recongnize isoleucine and leucine.
This is because their mass are same; therefore, this option assumes that isoleucines in a peptide can be interpreted as leucine, vice versa.
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Protein Database Mapping
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Supported protein database
To filter out known peptides, reference protein database mapping is useful.
This mapping is only for filtering out, not for mapping.
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Single amino acid variations
When map peptides on a reference protein database, it can be consider single amino acid variations (SAVs).
This option is useful for the sake of automatically detecting possible SAVs
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Variant Splice Graph Mapping
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Variant Splice Graph
ACTG supports variants such as single exon skipping, splice junction variation, frame shift, and exon-extension (mapping on exon and intron both).
Variant splice graph is built from reference human genome and transcriptome models and this information is separated by comma i.e. ReferenceGenomeVersion,TranscriptomeModelVersion.
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Mutations
If a user want to map mutations, the user must provide mutation information formatted VCF. The format is followed below.
1 32670862 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:48,0:.:48:0.00:0 41 36 5 51 46 5 Somatic
1 52553790 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:22,0:.:22:0.00:0 90 90 0 11 8 3 Somatic
1 75039014 . C A . DP NT=ref;QSS=160;QSS_NT=160;SGT=CC->AC;SOMATIC;TQSS=2;TQSS_NT=2 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 384:1:0:0:0,0:383,384:0,0:0,0 1 1 0 293 273 20 Somatic
Each field must be deliminated by tab, and the number of fields are at least 10.
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Exon Skipping
It automatically detects single exon skipping variation if it turns on.
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Alternative Acceptor & Donor
It automatically detects splice junction varaition if it turns on.
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Intron Mapping
It automatically detects exon-extension by mapping peptides on exon and intron both if it turns on.
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Six-frame Translation Mapping
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Reference genome
Support two reference human genome: GRCh37, GRCh38.
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