QuateXelero – Fast Motif Detection algorithm

QuateXelero

:: DESCRIPTION

QuateXelero is an extremely fast motif detection algorithm which has a Quaternary Tree data structure in the heart.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 QuateXelero

:: MORE INFORMATION

Citation

PLoS One. 2013 Jul 18;8(7):e68073. doi: 10.1371/journal.pone.0068073. Print 2013.
QuateXelero: an accelerated exact network motif detection algorithm.
Khakabimamaghani S1, Sharafuddin I, Dichter N, Koch I, Masoudi-Nejad A.

ExomeCopy 1.32.0 – Copy Number Variant Detection from Exome Sequencing Read Depth

ExomeCopy 1.32.0

:: DESCRIPTION

ExomeCopy implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

::DEVELOPER

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ExomeCopy

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1).
Modeling read counts for CNV detection in exome sequencing data.
Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.

Emap2sec – Protein secondary structure detection in intermediate-resolution cryo-EM maps

Emap2sec

:: DESCRIPTION

Emap2sec is a deep learning-based tool for detecting protein secondary structures from intermediate resolution cryo-EM maps.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Emap2sec

:: MORE INFORMATION

Citation

Nat Methods. 2019 Sep;16(9):911-917. doi: 10.1038/s41592-019-0500-1. Epub 2019 Jul 29.
Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning.
Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D.

PSE-HMM v1 – Genome-wide CNV detection from Next Generation Sequencing data

PSE-HMM v1

:: DESCRIPTION

PSE-HMM is a tool for the genome-wide CNV detection from Next Generation Sequencing data (mate pair reads). PSE-HMM applies an HMM with Position-Specific Emission probabilities for modeling different aberrations in the mate pairs, after being mapped to the reference genome.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

PSE-HMM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Nov 3;18(1):30. doi: 10.1186/s12859-016-1296-y.
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.
Malekpour SA, Pezeshk H, Sadeghi M

NetGSRforGGInt – Detection of Gene-Gene Interactions

NetGSRforGGInt

:: DESCRIPTION

NetGSRforGGInt is the algorithm that implemented the network-guided sparse regression for interaction detection

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package

:: DOWNLOAD

 NetGSRforGGInt

:: MORE INFORMATION

Citation

Lu, C., Latourelle, J., O’Connor, G.T., Dupuis, J., and Kolaczyk, E.D. (2013).
Network-guided sparse regression modeling for detection of gene-by-gene interactions.
Bioinformatics, 29(10), 1241-1249.

TrueSight 0.06 – Self-training Algorithm for Splice Junction Detection using RNA-seq

TrueSight 0.06

:: DESCRIPTION

TrueSight is a self-training algorithm for splice junction detection using RNA-seq

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TrueSight

:: MORE INFORMATION

Citation

Li Y, Li H, Burns P, Borodovsky M, Robinson GE, and Ma J.
TrueSight: self-training algorithm for splice junction detection using RNA-seq.
To appear in Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2012.

IMSindel – Intermediate-size Indel Detection tool

IMSindel

:: DESCRIPTION

IMSindel is an accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Ruby

:: DOWNLOAD

IMSindel

:: MORE INFORMATION

Citation

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.
Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T.
Sci Rep. 2018 Apr 4;8(1):5608. doi: 10.1038/s41598-018-23978-z. Erratum in: Sci Rep. 2018 Jul 4;8(1):10367.

ArtiFuse v1.0.0 – Computational Validation of Fusion Gene Detection tools without relying on simulated reads

ArtiFuse v1.0.0

:: DESCRIPTION

ArtiFusion is a tool to simulate artificial fusion events by modifying a given reference genome. The tool copies parts of the exonic sequence of gene A within the reference genome FASTA sequence into the downstream region of gene B and replaces the copied regions of gene A with Ns. The breakpoints are defined by using a size ratio between gene A and gene B and are always placed on exon-exon junctions. Intronic and intergenic regions remain unchanged.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

ArtiFuse

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Aug 2. pii: btz613. doi: 10.1093/bioinformatics/btz613.
ArtiFuse – Computational validation of fusion gene detection tools without relying on simulated reads.
Sorn P, Hohlsträter C, Löwer M, Sahin U, Weber D.

SAD – Salmon Anomaly Detection

SAD

:: DESCRIPTION

SAD detects the potential misquantifications for the RNA-seq transcript expression estimation made by Salmon. SAD detects large deviation of the observed coverage distribution from the expected coverage distribution for each transcript, and use the deviation as an indicator of misquantifications.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

SAD

:: MORE INFORMATION

Citation

Cong Ma, Carl Kingsford (2019).
Detecting, categorizing, and correcting coverage anomalies of RNA-seq quantification.
Cell Systems, in press..

SQUID v1.5 – Structural Variant Detection from RNA-seq

SQUID v1.5

:: DESCRIPTION

SQUID is designed to detect both fusion-gene and non-fusino-gene transcriptomic structural variations from RNA-seq alignment.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

SQUID

:: MORE INFORMATION

Citation

Genome Biol. 2018 Apr 12;19(1):52. doi: 10.1186/s13059-018-1421-5.
SQUID: transcriptomic structural variation detection from RNA-seq.
Ma C, Shao M, Kingsford C.