miRbiom – A Machine Learning Approach to Profile miRNAs

miRbiom

:: DESCRIPTION

miRbiom: Machine-Learning on Bayesian Causal Nets of RBP-miRNA interactions successfully predicts miRNA profiles

::DEVELOPER

SCBB-LAB (Studio of Computational Biology and Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

miRbiom

:: MORE INFORMATION

Citation

Pradhan UK, Sharma NK, Kumar P, Kumar A, Gupta S, Shankar R.
miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.
PLoS One. 2021 Oct 12;16(10):e0258550. doi: 10.1371/journal.pone.0258550. PMID: 34637468; PMCID: PMC8509996.

BnpC – Bayesian non-parametric Clustering of Single-cell Mutation Profiles

BnpC

:: DESCRIPTION

BnpC is a novel non-parametric method to cluster individual cells into clones and infer their genotypes based on their noisy mutation profiles.

::DEVELOPER

Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Python

:: DOWNLOAD

BnpC

:: MORE INFORMATION

Citation:

Borgsmüller N, Bonet J, Marass F, Gonzalez-Perez A, Lopez-Bigas N, Beerenwinkel N.
BnpC: Bayesian non-parametric clustering of single-cell mutation profiles.
Bioinformatics. 2020 Dec 8;36(19):4854-4859. doi: 10.1093/bioinformatics/btaa599. PMID: 32592465; PMCID: PMC7750970.

TIPMaP – Transcript Isoform Profiles from Microarray Probes

TIPMaP

:: DESCRIPTION

TIPMaP is a tool developed to identify differentially regulated transcripts (specific to human, mouse and rat).

::DEVELOPER

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS, Acharya KK.
TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
BMC Genomics. 2013 Dec 27;14:922. doi: 10.1186/1471-2164-14-922. PMID: 24373374; PMCID: PMC3884118.

FastTree 2.1.11 – Cmpute Large Minimum Evolution Trees with Profiles

FastTree 2.1.11

:: DESCRIPTION

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

::DEVELOPER

by Morgan N. Price in The Arkin laboratory .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

FastTree

:: MORE INFORMATION

Citation

Price, M.N., Dehal, P.S., and Arkin, A.P. (2009)
FastTree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix.
Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077.

Price, M.N., Dehal, P.S., and Arkin, A.P. (2010)
FastTree 2 — Approximately Maximum-Likelihood Trees for Large Alignments.
PLoS ONE, 5(3):e9490. doi:10.1371/journal.pone.0009490.

dRHP-PseRA – Detecting Remote Homology Proteins using Profile-based Pseudo Protein Sequence and Rank Aggregation

dRHP-PseRA

:: DESCRIPTION

dRHP-PseRA is a new predictor which was developed by combining four state-of-the-art predictors (PSI-BLAST, HHblits, Hmmer, and Coma) via the rank aggregation approach, based on the concept of pseudo proteins.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Chen J, Long R, Wang XL, Liu B, Chou KC.
dRHP-PseRA: detecting remote homology proteins using profile-based pseudo protein sequence and rank aggregation.
Sci Rep. 2016 Sep 1;6:32333. doi: 10.1038/srep32333. PMID: 27581095; PMCID: PMC5007510.

pHMM-Tree – Phylogeny of Profile hidden Markov models

pHMM-Tree

:: DESCRIPTION

pHMM-Tree is the first software to generate a phylogeny of profile hidden markov models (HMMs).

::DEVELOPER

YIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

pHMM-Tree 

:: MORE INFORMATION

Citation

Huo L, Zhang H, Huo X, Yang Y, Li X, Yin Y.
pHMM-tree: phylogeny of profile hidden Markov models.
Bioinformatics. 2017 Apr 1;33(7):1093-1095. doi: 10.1093/bioinformatics/btw779. PMID: 28062446; PMCID: PMC5860389.

NGS-Trex – NGS TRanscriptome profile EXplorer

NGS-Trex

:: DESCRIPTION

NGS-Trex is an automatic system for the analysis of NGS-Seq data.

::DEVELOPER

NGS-Trex team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 7:S10. doi: 10.1186/1471-2105-14-S7-S10. Epub 2013 Apr 22.
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer.
Boria I1, Boatti L, Pesole G, Mignone F.

PathRacer 3.15.0 – Racing Profile HMM Paths on Assembly Graph

PathRacer 3.15.0

:: DESCRIPTION

PathRacer is a novel standalone tool that aligns profile HMM directly to the assembly graph (performing the codon translation on fly for amino acid pHMMs). The tool provides the set of most probable paths traversed by a HMM through the whole assembly graph, regardless whether the sequence of interested is encoded on the single contig or scattered across the set of edges, therefore significantly improving the recovery of sequences of interest even from fragmented metagenome assemblies.

::DEVELOPER

Center for Algorithmic Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python

:: DOWNLOAD

PathRacer

:: MORE INFORMATION

PanGP 1.0.1 – Pan-Genome Profile Analyze Tool

PanGP 1.0.1

:: DESCRIPTION

PanGP is a tool for quickly analyzing bacterial pan-genome profile. It has integrated two kinds of sample algorithm, so that it could calculate the pan-genome profile of a population with dozens of or hundreds of strains at extremely low time-cost. At the same time, a user-friendly graphical interface was designed and the image about pan-genome profile could be drawn by PanGP directly.

::DEVELOPER

Yongbing Zhao 

:: SCREENSHOTS

PanGP

:: REQUIREMENTS

  • Linux/ Windows
  • Qt
  • openGL
  • C++ compiler

:: DOWNLOAD

 PanGP

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1297-9. doi: 10.1093/bioinformatics/btu017. Epub 2014 Jan 13.
PanGP: a tool for quickly analyzing bacterial pan-genome profile.
Zhao Y1, Jia X, Yang J, Ling Y, Zhang Z, Yu J, Wu J, Xiao J.

ORION – Profile-profile Fold Recognition

ORION

:: DESCRIPTION

ORION (Optimized fold RecognitION) is a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ORION

:: MORE INFORMATION

Citation

Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.
Ghouzam Y, Postic G, de Brevern AG, Gelly JC.
Bioinformatics. 2015 Aug 7. pii: btv462.