WildSpan protocols

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WildSpan specifications

Information


Unique identifier OMICS_26300
Name WildSpan
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Maintained No

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Publication for WildSpan

WildSpan in pipelines

 (2)
2007
PMCID: 1892096
PMID: 17570867
DOI: 10.1186/1471-2105-8-S5-S8

[…] of gap constraints for different purposes improves the efficiency of mining process while keeping high accuracy of mining results., the constraint model of magiic has been refined in our recent work wildspan [] to enhance the capability of the mining algorithm in discovering functional motifs for a specific query protein. wildspan restricts the length of intra-block gaps to be fixed, […]

2007
PMCID: 1892096
PMID: 17570867
DOI: 10.1186/1471-2105-8-S5-S8

[…] projects a sequence database into a smaller search space and grows patterns only in each projected database. both features contribute to favorable mining efficiency. at the end of the second phase, wildspan outputs the complete set of patterns that satisfy all the constraints specified by the users. the readers can refer to [] for the details of the algorithm and [] for the web server […]


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WildSpan in publications

 (3)
PMCID: 3413685
PMID: 22879883
DOI: 10.1371/journal.pone.0040950

[…] on e1ds motifs derived using the following procedures. different sequences relating to the same ec number were grouped, and mining for a sequential pattern was conducted for motif discovery using wildspan . before motif discovery the isotigs were translated using six all possible reading frames to generate peptide sequences, all of which were analyzed. the performance of wildspan to make […]

PMCID: 3005934
PMID: 21143803
DOI: 10.1186/1471-2164-11-S4-S2

[…] biologists reveal important site-directed mutagenesis in wet-lab experiments., the proposed prediction framework named “proterna” combines a svm-based classifier with conserved residue discovery by wildspan to identify the residues that interact with rna in a rna-binding protein. although these conserved residues can be either functionally conserved residues or structurally conserved residues, […]

PMCID: 1892096
PMID: 17570867
DOI: 10.1186/1471-2105-8-S5-S8

[…] of conserved residues in a set of protein sequences is important after introducing the concept of cluster-like patterns and the detailed mining procedures., we call a pattern generated by wildspan a cluster-like pattern. the residues inside a pattern are always clustered into several sequential blocks. the gaps in between two blocks are usually large and irregular. here comes […]


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WildSpan institution(s)
Department of Computer Science and Information Engineering, Ching Yun University, Taiwan; Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan; Department of Computer Science and Engineering, Yuan Ze University, Taiwan
WildSpan funding source(s)
Supported by National Science Council under contract number 98-2221-E-002-137-MY2, 99-2627-B-002-004, and 99-2221-E231-030.

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