This guide will give you a quick look at how to using SVAP on line web tools.
If you want to run SVAP on your computer, please refer to our
Installation Guide.
This guide will give you a quick look at how to using SVAP on line web tools.
If you want to run SVAP on your computer, please refer to our
Installation Guide.
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Online Assembler
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We provide an online isoform assembler as well as the standalone package.
User may upload their transcripts data to do online assembling. The online
assembler supports GFF, PSL and ECS data format as input data format.
The results can also be viewed in table format, graphical format or
SVAP alt raw data file. To know more about the data format, refer to our
Data Format Guide.
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Email
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Because of the complexity of alternative splicing, the splice graph could be
rather complicated, e.g. the Drosophila Dscam gene has about 38,000 potential
isoforms (Heber, et al., 2002), it might takes hours or days to do assembling.
By providing email address here, users can recieve their results by email for
those long-time runing assembling.
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Splice Mismatch
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Since most current est mapping to genome programs can not
ensure exact mapping coordinates, SVAP assembler need to
abide the slight difference of exon boundaries. Thus if two exons
start-boundaries/end-boundaries coordinates distance less than
Splice Mismatch, they will be treated as one same
coordinate.
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PolyA Mismatch
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An EST or mRNA having polyA tail or reliable polyA signal indicates the last exon
has a higher sequencing quality. Thus the splice mismatch of the last exon which
has the polyA tail or signal might be less than those do not have. So we allow
users specify a smaller mismatch value for this kind of exons.
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SameGene Mismatch
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SVAP groups input transcripts (ESTs & mRNAs) to genes by
exon overlapping standard (Engstrom, et al., 2006)
or common splicing juntcions standard (Yan annd Marr, 2005).
Each standard is based on the transcripts coordinates on chromosome,
because of the above reason, we also need a coordinates mismatch value
for grouping transcripts.
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Tiny Exon
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A too short exon may be a fake exon by error EST/mRNA sequencing or mapping.
SVAP assembler will ignore exons shorter than Tiny Exon value.
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Tiny Intron
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A too short intron may be a fake exon by error EST/mRNA sequencing or mapping.
SVAP assembler will ignore exons shorter than Tiny Intron value.
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Max DAG Path Number
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Cluster Name
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User can specify a Cluster Name for the input transcripts, it will be used
to name assembled isoforms.
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Task ID
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SVAP online assembler will automatically assign an unique ID for each
assembling task. Users can use the Task ID to retrieve their assemble
results.
NOTES: Task ID may be expired
after 7 days when it is created. The results of an expired task will removed from
the SVAP server and can not be retrieved.
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Table View
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The table view of assembling results. The format is easy to understand.
There are only one field needs to be explained --
The EXON value string like "exon-0: 6423946,6422996,%3=2,0.133": exon-0 means the exon is the first exon of the isoform, 6423946 and 6422996 are the start and end coordinates of the exon. %3=2 means the exon's length%3 = 2. 0.133 is the EST density of the exon. -
Gene Centric Display Mode
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This mode will display all assembled isoforms of your results.
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Variant Centric Display Mode
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This mode will display your specified isoform and its evidence transcripts.
The online graphical tool reads
the IDs from the alt results given by the online assembler automatically.
Users can select the one they want to look into.
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Variant ID
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To select the id of your results isoforms.
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width
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The width (unit pixel) of your graphical view's image. Leave blank for
default settings.
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height
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The height (unit pixel) of your graphical view's image. Leave blank for
default settings.
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Species
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The Species of your input transcripts. This can not be specified automatically
by the online view tool. Users should select the species themselves.
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Chromosome
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The chromosome of your input transcripts. It is a required option. Format is
chr + chromosome_number, eg. ( chr1, chr22, chrX, chrY ). If the chromosome
information is provided by the input data ( for example, an GFF attribute:
chr chr7; the PSL also provides the chromosome information.), the online graphical
view tool can assign the chromosome automatically, otherwise users should specify
the chromsome themselves. If the chromosome is not given, the web browser will give
an prompt box asks users to specify the chromosome.
