Software
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[http://zhanglab.c2b2.columbia.edu/index.php/OLego OLego] is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data. | [http://zhanglab.c2b2.columbia.edu/index.php/OLego OLego] is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data. | ||
| − | This work was published on NAR 2013. | + | This work was published on NAR 2013. [http://www.ncbi.nlm.nih.gov/pubmed/23571760 Link] |
=SpliceTrap= | =SpliceTrap= | ||
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[[Image:splicetrap.jpg |300px]] | [[Image:splicetrap.jpg |300px]] | ||
| − | [http:// | + | [http://splicetrap.sf.net/ SpliceTrap] is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads. |
This work was published on Bioinformatics, 2011 [http://bioinformatics.oxfordjournals.org/content/27/21/3010.long Link] | This work was published on Bioinformatics, 2011 [http://bioinformatics.oxfordjournals.org/content/27/21/3010.long Link] | ||
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[[Image:BSSF.png |300px]] | [[Image:BSSF.png |300px]] | ||
| − | BSSF(Binding Site Similarity & Function) enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method. | + | [http://202.127.30.184:8080/jwu/index.jsp BSSF] (Binding Site Similarity & Function) was developed when I was working in Shanghai Institute of Materia Medica. It enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method. |
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Latest revision as of 22:07, 25 August 2014
[edit] OLego
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data.
This work was published on NAR 2013. Link
[edit] SpliceTrap
SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.
This work was published on Bioinformatics, 2011 Link
[edit] BSSF
BSSF (Binding Site Similarity & Function) was developed when I was working in Shanghai Institute of Materia Medica. It enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method.