MAPanalyzer – Analyzing Microtubule-associated Proteins

MAPanalyzer

:: DESCRIPTION

MAPanalyzer is a MAP (Microtubule-associated Proteins) analysis tool.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins.
Zhou Y, Yang S, Mao T, Zhang Z.
Database (Oxford). 2015 Nov 13;2015. pii: bav108. doi: 10.1093/database/bav108.

xMAN 20060925 – MAp OligoNucleotides to Subject Genome

xMAN 20060925

:: DESCRIPTION

xMAN (extreme MApping of OligoNucleotides) is a simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length. xMAN is at least an order of magnitude faster than other popular existing tools.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  xMAN

:: MORE INFORMATION

Citation:

Li W, Carroll JS, Brown M, Liu S.
xMAN: extreme MApping of OligoNucleotides.
BMC Genomics. 2008;9 Suppl 1:S20.

CREST 1.0.1 – uses the soft-clipped reads to directly Map the Breakpoints of SVs

CREST 1.0.1

:: DESCRIPTION

CREST (clipping reveals structure) is an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  CREST

:: MORE INFORMATION

Citation

Jianmin Wang et al.
CREST maps somatic structural variation in cancer genomes with base-pair resolution
Nature Methods 8, 652–654 (2011)

NextGenMap 0.5.5 – Map NGS Reads against a Reference Genome

NextGenMap 0.5.5

:: DESCRIPTION

NextGenMap/NGM (Next Generation Mapper)is a computer program to map NGS reads against a reference genome using CPUs or GPUs.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NextGenMap

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468.
NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
Sedlazeck FJ, Rescheneder P, von Haeseler A.

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.

rMAPS 2.0.0 – RNA Map analysis and Plotting server for alternative Exon Regulation

rMAPS 2.0.0

:: DESCRIPTION

rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.

::DEVELOPER

rMAPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

rMAPS: RNA map analysis and plotting server for alternative exon regulation.
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.
Nucleic Acids Res. 2016 May 12. pii: gkw410.

PLABQTL 20100816 – computer program to Map QTL

PLABQTL 20100816

:: DESCRIPTION

PLABQTL (PLAnt Breeding QTL analysis)is a program written for the detection of loci which affect the variation of quantitative traits. Its main purpose is to localize and characterize QTL (Quantitative
Trait Loci).

::DEVELOPER

H. Friedrich Utz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • windows

:: DOWNLOAD

PLABQTL

:: MORE INFORMATION

Citation

Utz and Melchinger, 1996:
PLABQTL: A program for composite interval mapping of QTL.
Journal of Agricultural Genomics 2, 1-5

elPrep 2.4 – High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

elPrep  2.4

:: DESCRIPTION

elPrep is a high-performance tool for preparing .sam/.bam/.cram files for variant calling in sequencing pipelines.It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with different pipelines for variant analysis with GATK.

::DEVELOPER

The Exascience Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 elPrep

:: MORE INFORMATION

Citation

PLoS One. 2015 Jul 16;10(7):e0132868. doi: 10.1371/journal.pone.0132868. eCollection 2015.
elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.
Herzeel C, Costanza P, Decap D, Fostier J, Reumers J

tfbs_species 1.0 – Map Human Transcription Factor Binding Sites to Another Species

tfbs_species 1.0

:: DESCRIPTION

The aim of tfbs_species is to translate a list of binding sites from the University of California Santa Cruz(UCSC) Genome database from one species to another. At the moment, this data only exists for the human genome

::DEVELOPER

Raymond Wan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  tfbs_species

:: MORE INFORMATION

PDB-Explorer – Web-based interactive Map of PDB in Shape Space

PDB-Explorer

:: DESCRIPTION

PDB-Explorer is a web application for the interactive visualization of chemical space of RCSB Protein Data Bank (PDB) characterized by protein shape fingerprint (3DP) and shape similarity search for molecules in PDB.

::DEVELOPER

PDB-Explorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PDB-Explorer: a web-based interactive map of the protein data bank in shape space.
Jin X, Awale M, Zasso M, Kostro D, Patiny L, Reymond JL.
BMC Bioinformatics. 2015 Oct 23;16(1):339.