SuRankCo R5 – Supervised Ranking of Contigs in de novo Assemblies

SuRankCo R5

:: DESCRIPTION

SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.

::DEVELOPER

SuRankCo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Java
R

:: DOWNLOAD

SuRankCo

:: MORE INFORMATION

Citation

Kuhring M, Dabrowski PW, Piro VC, Nitsche A, Renard BY.
SuRankCo: supervised ranking of contigs in de novo assemblies.
BMC Bioinformatics. 2015 Jul 30;16:240. doi: 10.1186/s12859-015-0644-7. PMID: 26224355; PMCID: PMC4520199.

ProtDet-CCH – Protein Remote Homology Detection by combining Long Short-Term Memory and Ranking methods

ProtDet-CCH

:: DESCRIPTION

ProtDet-CCH is a Python package for Protein remote homology detection by combining Long Short-Term Memory and ranking methods

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
Python

:: DOWNLOAD

ProtDet-CCH i

:: MORE INFORMATION

Citation

Liu B, Li S.
ProtDet-CCH: Protein Remote Homology Detection by Combining Long Short-Term Memory and Ranking Methods.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1203-1210. doi: 10.1109/TCBB.2018.2789880. Epub 2018 Jan 5. PMID: 29993950.

CONSRANK – Analysis,Comparison and Ranking of Docking Models based on Inter-residue Contacts

CONSRANK

:: DESCRIPTION

CONSRANK (CONSensus-RANKing) is a web service to easily and effectively analyse and rank docking models of protein-protein and protein-nucleic acid complexes, based on the frequency of inter-residue contacts.

::DEVELOPER

MoLNaC: Modeling Lab for Nanostructures and Catalysis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

WEb Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts.
Chermak E, Petta A, Serra L, Vangone A, Scarano V, Cavallo L, Oliva R.
Bioinformatics. 2014 Dec 21. pii: btu837.

SaRa 1.1 – Sreening and Ranking algorithm for CNV detection

SaRa 1.1

:: DESCRIPTION

SaRa is a program to detect chromosome copy number variations.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
R

:: DOWNLOAD

SaRa

:: MORE INFORMATION

Citation

Niu and Zhang.
The screening and ranking algorithm to detect DNA copy number variations.
Ann. Appl. Stat. 6,1306-1326, (2012).

modSaRa 1.0 — Modified Sreening and Ranking algorithm for CNV detection

modSaRa 1.0

:: DESCRIPTION

modSaRa is a program using modified screening and ranking algorithm to detect chromosome copy number variations. It is an optimal and accurate approach solving practical issues regarding CNV detection.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux /MacOsX
R

:: DOWNLOAD

modSaRa

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Dec 25. pii: btu850. [Epub ahead of print]
Modified Screening and Ranking Algorithm for Copy Number Variation Detection.
Xiao F, Min X, Zhang H

ReliefSeq – Ranking Features of Genetic Sequence data using Relief-F

ReliefSeq

:: DESCRIPTION

ReliefSeq is a feature (attribute) selection and ranking algorithm written in C++ designed to handle various types of genetic features including combinations of feature data types and endpoints (phenotypes/classes).

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ReliefSeq

:: MORE INFORMATION

Citation

PLoS One. 2013 Dec 10;8(12):e81527. doi: 10.1371/journal.pone.0081527. eCollection 2013.
ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.
McKinney BA, White BC, Grill DE, Li PW, Kennedy RB, Poland GA, Oberg AL.

DOCKSCORE – Ranking Protein-protein Docked Poses

DOCKSCORE

:: DESCRIPTION

DockScore is a rigorous scoring scheme which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed.

::DEVELOPER

DockScore Team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

DOCKSCORE: a webserver for ranking protein-protein docked poses.
Malhotra S, Mathew OK, Sowdhamini R.
BMC Bioinformatics. 2015 Apr 24;16(1):127.

ProRank 0.1 – Detection of Protein Complexes using a Protein Ranking algorithm.

ProRank 0.1

:: DESCRIPTION

ProRank is a novel method for detecting protein complexes from PPI by using a protein ranking algorithm. ProRank quantifies the importance of each protein based on the interaction structure and the evolutionarily relationships between proteins in the network.

::DEVELOPER

Nazar Zaki , Bioinformatics Laboratory, UAE University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows / Linux/ MacOsX
Python
Numpy

:: DOWNLOAD

ProRank

:: MORE INFORMATION

Citation

Proteins. 2012 Oct;80(10):2459-68. doi: 10.1002/prot.24130.
Detection of protein complexes using a protein ranking algorithm.
Zaki N, Berengueres J, Efimov D.

STOVCA 3.95 – Comparison, Ranking and Evaluation of Structure Alignments

STOVCA 3.95

:: DESCRIPTION

STOVCA (STructural OVerlap CAlculator) is a software that takes as input a pairwise structure superposition of proteins, DNA or RNA in PDB format generated by any software and produces a standardized structural alignment and its corresponding similarity measures, according to the parameters provided by the user. Therefore, STOVCA allows the direct comparison and ranking of structural superpositions generated by any structure superposition software

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX

:: DOWNLOAD

STOVCA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):47-53. doi: 10.1093/bioinformatics/bts600. Epub 2012 Oct 11.
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments.
Slater AW1, Castellanos JI, Sippl MJ, Melo F.

MORPH / MORPH-R 10.7 – MOdule guided Ranking of Candidate PatHway Genes

MORPH / MORPH-R 10.7

:: DESCRIPTION

MORPH is an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities

MORPH-R is Morph R package.

::DEVELOPER

Ron Shamir’s lab and Eleanore Wurtzel’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

MORPH , MORPH-R

:: MORE INFORMATION

Citation

Tzfadia, O., Amar, D., Bradbury, L.M.T., Wurtzel, E.T., and Shamir, R. (2012)
The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana and Solanum lycopersicum pathways.
Plant Cell. 2012 Nov;24(11):4389-406. doi: 10.1105/tpc.112.104513.

Physiol Plant. 2015 Jan 27. doi: 10.1111/ppl.12326. [Epub ahead of print]
The MORPH-R web server and software tool for predicting missing genes in biological pathways.
Amar D, Frades I, Diels T, Zaltzman D, Ghatan N, Hedley PE, Alexandersson E, Tzfadia O, Shamir R.