scikit-bio 0.5.5 – Python 3 package providing Data Structures, Algorithms and Educational Resources for Bioinformatics

scikit-bio 0.5.5

:: DESCRIPTION

scikit-bio is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

scikit-bio

:: MORE INFORMATION

GeneStitch 1.2.1 – Network Matching Algorithm to Gene Assembly

GeneStitch 1.2.1

:: 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

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  GeneStitch

:: 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.

BOQA – Bayesian Ontology Query Algorithm

BOQA

:: DESCRIPTION

BOQA integrates the knowledge stored in an ontology and the accompanying annotations into a Bayesian network in order to implement a search system in which users enter one or more terms of the ontology to get a list of appropriate domain items.

::DEVELOPER

Phenomics Berlin Home

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BOQA

:: MORE INFORMATION

Citation

Sebastian Bauer, Sebastian Köhler, Marcel H. Schulz and Peter N. Robinson
Bayesian Ontology Querying for Accurate and Noise-Tolerant Semantic Searches
Bioinformatics (2012) doi: 10.1093/bioinformatics/b

LaJolla 2.2.1 – Peer Reviewed Algorithm for the 3D Alignment

LaJolla 2.2.1

:: DESCRIPTION

LaJolla is a peer reviewed algorithm for the 3D alignment of RNA and protein structures. It uses n-gram based indexing and produces a set of 3D superpositions to found substructures.LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested.

::DEVELOPER

LaJolla Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

LaJolla

:: MORE INFORMATION

Citation

Bauer, R.; Rother, K.; Moor, P.; Reinert, K.; Steinke, T.; Bujnicki, J. M.; Preissner, R.
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors.
Algorithms 2009, 2, 692-709.

NRProF – Protein Function Prediction Based on the Neural Response Algorithm

NRProF

:: DESCRIPTION

 NRProF is a novel automated protein functional assignment method based on the neural response algorithm, which simulates the neuronal behavior of the visual cortex in the human brain. The main idea of this algorithm is to define a distance metric that corresponds to the similarity of the subsequences and reflects how the human brain can distinguish between different sequences. We predicted the most similar target protein for a given query protein using the two layered neural response algorithm and thereby assigned the GO term associated with the target sequence to the query sequence. Our method predicted and ranked the actual GO term in the first position out of five with an accuracy of 82%. Results of the 5-fold cross validation and the comparison with PFP server indicate the better performance by our method.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package

:: DOWNLOAD

 NRProF

:: MORE INFORMATION

Citation

Hari Krishna Yalamanchili, Quan-Wu Xiao, and Junwen Wang .
A novel neural response algorithm for protein function prediction
BMC Systems Biology 2012, 6(Suppl 1):S19

LightAssembler – Lightweight Resources Assembly Algorithm

LightAssembler

:: DESCRIPTION

LightAssembler is a lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other holding k-mers classified as likely correct, using a simple statistical test.

::DEVELOPER

Sara El-Metwally

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LightAssembler

:: MORE INFORMATION

Citation

LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.
El-Metwally S, Zakaria M, Hamza T.
Bioinformatics. 2016 Jul 13. pii: btw470.

CHIAMANTE 1.0.3 – Joint Genotype Calling algorithm for Array and Sequence data

CHIAMANTE 1.0.3

:: DESCRIPTION

Chiamante is a genotype caller for Illumina Beadchips that can augment microarray data with genotype likelihoods from sequence data for improved genotype accuracy and call rate. Whilst primarily designed to call genotypes via fusing these two sources of information, Chiamante also functions as a highly accurate array-only caller.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHIAMANTE

:: MORE INFORMATION

Citation

J O’Connell, J. Marchini (2012)
Joint Genotype Calling With Array and Sequence Data.
Genetic Epidemiology. 10.1002/gepi.21657

ProPhylo 1.02 – Phylogenetic Profile comparison program using Partial Phylogenetic Profile algorithm

ProPhylo 1.02

:: DESCRIPTION

ProPhylo is a high-performance parallel software to run phylogenetic profile searches at genome-scale.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  ProPhylo

:: MORE INFORMATION

Citation

Basu, M. K., Selengut, J. D., Haft, D. H.
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
BMC Bioinformatics. 2011 Dec 01; 12: 434.

MeDiChI 0.4.1 – Model-Based ChIP-chip Deconvolution Algorithm

MeDiChI 0.4.1

:: DESCRIPTION

MeDiChI is method for the automated, model-based deconvolution of protein-DNA binding (Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray — ChIP-chip) data that discovers DNA binding sites at high resolution (higher resolution than that of the tiling array itself).

::DEVELOPER

Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 MeDiChI

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.
Model-based deconvolution of genome-wide DNA binding.
Reiss DJ, Facciotti MT, Baliga NS.

reHCstar 2.1.3 – Algorithm for Haplotype Inference problem on Pedigree data with Recombinations, Errors and Mutations

reHCstar 2.1.3

:: DESCRIPTION

reHCstar is a SAT-based program to compute a haplotype configuration on pedigrees with recombinations, genotyping errors, and missing genotypes.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • CMake
  • GNU make
  • Boost FileSystem, System, DateTime, ProgramOptions, IOStreams, and other include-only libraries
  • Apache Log4cxx

:: DOWNLOAD

 reHCstar

:: MORE INFORMATION

Citation

Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, and Paola Bonizzoni.
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2012).