:: DESCRIPTION
HDMC is a novel deep learning based framework for batch effect removal in scRNA-seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Wang X, Wang J, Zhang H, Huang S, Yin Y.
HDMC: a novel deep learning based framework for removing batch effects in single-cell RNA-seq data.
Bioinformatics. 2021 Dec 4:btab821. doi: 10.1093/bioinformatics/btab821. Epub ahead of print. PMID: 34864918.
:: DESCRIPTION
PSMAlign is an open source tool that performs pairwise RNA secondary structures alignment based on the conserved stem pattern discovered. It enables alignment of large structures, such as those in the 23S ribosomal RNA family. Arbitrary pseudoknots are also allowed.
::DEVELOPER
Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pairwise RNA secondary structure alignment with conserved stem pattern.
Chiu JK, Chen YP.
Bioinformatics. 2015 Aug 13. pii: btv471.
:: DESCRIPTION
GeneMatcher is a freely accessible web site designed to enable connections between clinicians and researchers from around the world who share an interest in the same gene or genes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
GeneMatcher: A Matching Tool for Connecting Investigators with an Interest in the Same Gene.
Sobreira N, Schiettecatte F, Valle D, Hamosh A.
Hum Mutat. 2015 Oct;36(10):928-30. doi: 10.1002/humu.22844.
:: DESCRIPTION
SIM (Spectrum Identification Machine) is a Peptide Spectrum Match – PSM search tool that capitalizes on the high intensity b1 fragment ion of tandem mass spectra of peptides coupled in solution with Phenylisotiocyanate – PITC to confidently sequence the first amino acid and ultimately reduce the search space. This tool enables to make a search with sample without PITC labeling too.
::DEVELOPER
Laboratory for Proteomics and Protein Engineering
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 May 15;29(10):1343-4. doi: 10.1093/bioinformatics/btt106. Epub 2013 Feb 27.
Effectively addressing complex proteomic search spaces with peptide spectrum matching.
Borges D1, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, Fran?a FM, Barbosa VC, Sánchez A, Carvalho PC.
:: DESCRIPTION
ContextShapes does rigid-body protein docking. It uses a novel contextshapes data structure to represent local surface regions/shapes on the protein. All critical points on both the receptor and ligand are represented via context shapes, and the best docking is found via pair-wise matching.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zujun Shentu, Mohammad Al Hasan, Chris Bystroff and Mohammad J. Zaki,
Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking.
Proteins: Structure, Function and Bioinformatics, 70(3):1056-1073. Feb 2008
:: DESCRIPTION
TPMS is a program suite for bioinformatics. It can manage phylogenetic tree collections, root them, query some peculiar pattern, and detect horizontal transfer.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
CitationBMC Bioinformatics. 2013 Mar 27;14:109. doi: 10.1186/1471-2105-14-109.
TPMS: a set of utilities for querying collections of gene trees.
Bigot T1, Daubin V, Lassalle F, Perrière G.
:: DESCRIPTION
VarMatch: robust matching of small variant datasets using flexible scoring schemes
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics, 33 (9), 1301-1308 2017 May 1
VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes
Chen Sun , Paul Medvedev
:: DESCRIPTION
ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs.
::DEVELOPER
Freiburg Bioinformatics Group.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen
In: Nucleic Acids Research, 2010, 38 Suppl, W373-7
:: DESCRIPTION
GeneStitch is a tool to assemble genes using network matching algorithm. Given an already-assembled dataset, it is capable of assembling contigs together to form more complete genes with the help of a reference gene set. Currently the assembly software that GeneStitch support is SOAPdenovo.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Sep 15;28(18):i363-i369. doi: 10.1093/bioinformatics/bts388.
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.
Wu YW, Rho M, Doak TG, Ye Y.
:: DESCRIPTION
PalCheck is a java program that supports both online palindrome pattern matching and online multiple palindrome pattern matching.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
OMPPM: Online Multiple Palindrome Pattern Matching.
Kim H, Han YS.
Bioinformatics. 2015 Dec 16. pii: btv738.
