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.

SPALN 2.3.3f – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence

SPALN 2.3.3f

:: DESCRIPTION

Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. Spaln adopts multi-phase heuristics that makes it possible to perform the job on a conventional personal computer running under Unix/Linux with limited memory. The program is written in C++ and distributed as source codes and also as executables for a few platforms. Unless binaries are not provided, users must compile the program on their own system. Although the program has been tested only on a Linux operating system, it is likely to be portable to most Unix systems with little or no modifications. The accessory program sortgrcd sorts the gene loci found by spaln in the order of chromosomal position and orientation.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 SPALN

:: MORE INFORMATION

Citation

Gotoh, O.
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
Nucleic Acids Research 36 (8) 2630-2638 (2008).

MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments

MIMEAnTo

:: DESCRIPTION

Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using the herein developed user-friendly, cross-platform software MIMEAnTo (MIME Analysis Tool).

::DEVELOPER

MIMEAnTo team

:: SCREENSHOTS

MIMEAnTo

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Gnuplot

:: DOWNLOAD

 MIMEAnTo

:: MORE INFORMATION

Citation:

MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments.
Smith MR, Smyth RP, Marquet R, von Kleist M.
Bioinformatics. 2016 Jul 10. pii: btw479.

SeqSaw 1.0.8 – Short Spliced Sequence Mapping Tool

SeqSaw 1.0.8

:: DESCRIPTION

SeqSaw is a package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

::DEVELOPER

SeqSaw team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SeqSaw

:: MORE INFORMATION

Citation

Biochem Biophys Res Commun. 2011 Jun 3;409(2):299-303. Epub 2011 May 7.
Observations on novel splice junctions from RNA sequencing data.
Wang L, Wang X, Wang X, Liang Y, Zhang X.

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