Pasqual 1.0 – Parallel de Novo Genome Sequence Assembler

Pasqual 1.0

:: DESCRIPTION

PASQUAL (PArallel SeQUence AssembLer) is designed for shared memory parallelism, using OpenMP due to its good tradeoff between performance and programmer productivity. Shared memory parallelism has become mainstream with the widespread production of multicore commodity processors. For PASQUAL we follow the OLC approach and use a careful combination of tailored algorithms and data structures to obtain high-quality solutions.

::DEVELOPER

Bader HPC Lab @ GeorgiaTech

:: REQUIREMENTS

Linux

:: DOWNLOAD

Pasqual

:: MORE INFORMATION

Citation

Xing Liu, Pushkar R. Pande, Henning Meyerhenke, and David A. Bader.
PASQUAL: A Parallel de novo Assembler for Next Generation Genome Sequencing.
Submitted for journal publication, 2011.

MADAP 2.0 – Clustering Tool for One-dimensional Genome Annotation Data Mapped onto Genome Sequences

MADAP 2.0

:: DESCRIPTION

MADAP is a flexible clustering tool for the interpretation of one-dimensional genome annotation data mapped onto complete or partial genome sequences. Such data might consist in counts, probabilities, or intensities and be obtained from cDNA and tag sequencing protocols to map the 5′ and 3’ends of mRNA, from ChIP-chip analysis, or from genome-wide SNP-typing used in genotype-phenotype association studies. MADAP identifies groups of data corresponding to one or several genomic sites, and estimates the volume and extension of such groups (clusters).

::DEVELOPER

Computational Cancer Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

MADAP

:: MORE INFORMATION

Citation

Schmid CD, Sengstag T, Bucher P and Delorenzi M. (2007)
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.
Nucleic Acids Res, 35, W201-205.

SPLITS 1.1 / SPLITSX – tRNA Detection in Genome Sequence

SPLITS 1.1 / SPLITSX

:: DESCRIPTION

SPLITS and SPLITSX, expansion programs for tRNAscan-SE to detect spliced-tRNA genes, such as split-tRNA genes (Figure A) and intron-containing tRNA genes (Figure B) in archaea.

The length of the query sequence should be limited within 5 mega base pairs (nucleotide). If your sequence is longer than this, please divide the sequence and submit separately. Finally these programs are under active development. If you use these programs, please help me out by e-mailing me with suggestions, comments, and bug reports.

::DEVELOPER

Institute for Advanced Biosciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Perl

:: DOWNLOAD

SPLITS / SPLITSX

:: MORE INFORMATION

Citation

Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, Kanai A. (2006).
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.
In Silico Biology. 6, 0039.

Sugahara J., Yachie N., Arakawa K., Tomita M. (2007)
In Silico Screening of Archaeal tRNA-encoding Genes Having Multiple Introns with Bulge-Helix-Bulge Splicing Motifs,
RNA; 13: 671-681