MetaMap 2020 – Mapping of Biomedical Text to the UMLS Metathesaurusext

MetaMap 2020

:: DESCRIPTION

MetaMap is a highly configurable program to map biomedical text to the UMLS Metathesaurus or, equivalently, to discover Metathesaurus concepts referred to in text. MetaMap uses a knowledge-intensive approach based on symbolic, natural-language processing (NLP) and computational-linguistic techniques. Besides being applied for both IR and data-mining applications, MetaMap is one of the foundations of NLM’s Medical Text Indexer (MTI) which is being used for both semiautomatic and fully automatic indexing of biomedical literature at NLM.

::DEVELOPER

Dr. Alan (Lan) Aronson at the National Library of Medicine (NLM)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux /Windows

:: DOWNLOAD

 MetaMap

:: MORE INFORMATION

Citation:

An overview of MetaMap: historical perspective and recent advances.
Aronson AR, Lang FM.
J Am Med Inform Assoc. 2010 May-Jun;17(3):229-36. doi: 10.1136/jamia.2009.002733.

CuReSim 1.3 / CuReSimEval 1.1 – Customized Read Simulator / Evaluate Mapping Quality of CuReSim Simulated Reads

CuReSim 1.3 / CuReSimEval 1.1

:: DESCRIPTION

CuReSim is a customized tool which generates synthetic New-Generation Sequencing reads, supporting read simulation for major letter-base sequencing platforms.

CuReSimEval is a tool to evaluate the mapping quality of the CuReSim simulated reads.

::DEVELOPER

CuReSim team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

 CuReSim , CuReSimEval

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.
Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.
Caboche S1, Audebert C, Lemoine Y, Hot D.

DamMet 1.0.2 – a full probabilistic model for Mapping Ancient Methylomes

DamMet 1.0.2

:: DESCRIPTION

DamMet is probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen. The model is implemented as a two step procedure. The first step recovers a maximum likelihood estimate (MLE) of the position specific deamination rates for methylated and unmethylated cytosine residues. The second step, making use of these deamination rates, returns a MLE of the methylation level in a user-defined genomic window. The software is multithreaded

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DamMet

:: MORE INFORMATION

Citation

Hanghoj K, Renaud G, Albrechtsen A, Orlando L.
DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.
Gigascience. 2019 Apr 1;8(4):giz025. doi: 10.1093/gigascience/giz025. PMID: 31004132; PMCID: PMC6474913.

BSMAP 2.90 – Whole Genome Bisulfite Sequence MAPping program

BSMAP 2.90

:: DESCRIPTION

BSMAP(Bisulfite Sequence Mapping Program)is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BSMAP

:: MORE INFORMATION

Citation:

BSMAP: whole genome bisulfite sequence MAPping program.
Xi Y, Li W.
BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.

Bioinformatics. 2012 Feb 1;28(3):430-2. doi: 10.1093/bioinformatics/btr668. Epub 2011 Dec 6.
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.
Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W.

Identitag – Tag-to-gene Mapping

Identitag

:: DESCRIPTION

Identitag is a tool called for tag-to-gene mapping. This tool is based on a relational database which structure can be depicted as three interconnected modules represented in Identitag relational schema. The first one stores virtual tags extracted from transcript sequences belonging to the species considered the second stores experimental tags observed in SAGE experiments, and the third allows the annotation of the transcript sequences used for virtual tag extraction. Identitag therefore connects an observed tag to a virtual tag and to the transcript sequence from which it is derived, and then to its functional annotation when available. For a complete description of Identitag tables see Identitag data dictionary.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux

:: DOWNLOAD

Identitag

:: MORE INFORMATION

Citation

Keime, C., Damiola, F., Mouchiroud, D., Duret, L. and Gandrillon, O. (2004)
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.
BMC Bioinformatics, 5, 143

CORA 1.1.5b – compressive-acceleration tool for NGS Read Mapping methods

CORA 1.1.5b

:: DESCRIPTION

CORA is a compressive-acceleration tool for NGS read mapping methods. When plugged into existing mapping tools, CORA achieves substantial runtime improvement through the use of compressive representation of the reads and a comprehensive homology map of the reference genome.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CORA

:: MORE INFORMATION

Citation:

Deniz Yorukoglu, Y. William Yu, Jian Peng, Bonnie Berger.
Compressive Mapping for Next-generation Sequencing
Nature Biotechnology 34, 374-376 (2016) doi:10.1038/nbt.3511.

MARIO 0.4 – Mapping RNA-RNA interactome and RNA Structure

MARIO 0.4

:: DESCRIPTION

MARIO (Mapping RNA-RNA interactome in vivo) is a tools to study RNA-RNA interactome and structures in vivo.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BioPython

:: DOWNLOAD

MARIO

:: MORE INFORMATION

Citation

Nat Commun. 2016 Jun 24;7:12023. doi: 10.1038/ncomms12023.
Mapping RNA-RNA interactome and RNA structure in vivo by MARIO.
Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S.

WMap 20091230 – Mapping of Sequence Reads

WMap 20091230

:: DESCRIPTION

WMap is a new sequence mapping software designed to map high-throughput sequencing reads as well as methylated-C reads, enabling usage of such sequencing data to various fields of biological research.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 WMap

:: MORE INFORMATION

Infomap Bioregions – Interactive mapping of Biogeographical Regions from Species Distributions

Infomap Bioregions

:: DESCRIPTION

Infomap Bioregions is an interactive web application that inputs species distribution data and generates bioregion maps.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Syst Biol. 2017 Mar 1;66(2):197-204. doi: 10.1093/sysbio/syw087.
Infomap Bioregions: Interactive Mapping of Biogeographical Regions from Species Distributions.
Edler D, Guedes T, Zizka A, Rosvall M, Antonelli A

Algpred – Prediction of Allergenic Proteins and mapping of IgE Epitopes

Algpred

:: DESCRIPTION

AlgPred is a web server which has been developed for the predicting allergenic proteins and for mapping IgE epitopes on allergenic proteins

::DEVELOPER

Algpred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W202-9.
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes.
Saha S1, Raghava GP.