Institute of Bioinformatics Münster
NanoPipe
2019/10/14 13:46
New Request
Previous Request
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ID
New Request
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Target
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Target File
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Query File
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Minimum Sequence Length
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Email
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Title
Last Parameters
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Substitution Matrix
Use Matrix or Match Score / Mismatch Cost
A C G T
A
C
G
T
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Match Score (-r)
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Mismatch Cost (-q)
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Gap Existence Cost (-a)
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Gap Extension Cost (-b)
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Insertion Existence Cost (-A)
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Insertion Extension Cost (-B)
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Score Matrix applies to Forward Strand (-S)
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Initial Matches Position (-k)
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Maximum Score Drop (-x)
You can enter an id of a previous run. Alternatively you can select one of the last 10 runs in the selection box.
Please select a target against you want to analyze. Some targets are already on the webserver and you don't need to upload a target file.
Select a target file in fasta format which will be uploaded to the server. This only works when target selection is "Upload File".
Select a query file which will be uploaded to the server. The file can be a single fasta or fastq file or an archive in gzip, bzip or zip format containing several fasta or fastq files.
The minimum length of the query seqeunces. If set to 0 it is disgarded.
If you want to be informed by email after the job is processesd.
You may give this job a title, to help you identify it later on. The job title will be carried on all subsequent displays.
Enter or load a substitution matrix. The button "init" and "default" mean to initilize the matrix either with 0 values or to initilize it with default values. If all values of the matrix are zero: it will be discarded and "Match Score" and "Mismatch Costs" are taken, that means the are exclusivly used.
By default, this pipeline uses a match score of 6 for "Dengue virus serotype classification". For "Plasmodium polymorphisms", the match score is defined by a specific substitution matrix (4 for A/T, 9 for C/G). The LAST default match score is 6.
By default, this pipeline uses a mismatch cost of 12 for "Plasmodium polymorphisms" and for "Dengue virus serotype classification". The LAST default mismatch cost is 18.
By default, this pipeline uses a gap existence cost of 12 for "Plasmodium polymorphisms" and for "Dengue virus serotype classification". The LAST default gap existence cost is 21.
By default, this pipeline uses a gap extension cost of 3 for "Plasmodium polymorphisms" and 4 for "Dengue virus serotype classification". The LAST default gap extension cost is 9.
By default, this pipeline uses a insertion existence cost of 15 for "Plasmodium polymorphisms" and for "Dengue virus serotype classification". By default, the LAST insertion existence cost is set to the same value as the gap existence cost (-a).
Insertion extension cost
Initial matches starting at every k-th position in each query
Maximum score drop for gapped alignments
Score matrix applies to forward strand of: 0=reference, 1=query