CLARK 1.2.3 – Fast and Accurate Classification of Metagenomic and Genomic Sequences

CLARK 1.2.3

:: DESCRIPTION

Clark is a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed.

::DEVELOPER

Rachid OunitAlgorithms and Computational Biology Lab ,University of California

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CLARK

:: MORE INFORMATION

Citation

Ounit R, Wanamaker S, Close TJ, Lonardi S,
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
BMC Genomics 2015, 16:236.

Trnascan-SE 2.0 – Search for tRNA Genes in Genomic Sequence

Trnascan-SE 2.0

:: DESCRIPTION

tRNAscan-SE is a program for improved detection of transfer RNA genes in genomic sequence.

::DEVELOPER

the Lowe Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Trnascan-SE

:: MORE INFORMATION

Citation:

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.
Lowe TM, Chan PP.
Nucleic Acids Res. 2016 May 12. pii: gkw413.

Lowe, T.M. and Eddy, S.R. (1997)
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Nucleic Acids Research, 25, 955-964.

RECON 1.05 – Identification of Repeat Families from Genomic Sequences

RECON 1.05

:: DESCRIPTION

The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.

::DEVELOPER

Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Windows
  • Perl 
  • C Compiler

:: DOWNLOAD

 RECON

:: MORE INFORMATION

Citation:

Bao Z. and Eddy S.R. (2002)
Automated de novo Identification of Repeat Sequence Families in Sequenced Genomes.
Genome Research, 12:1269-1276.

UNWORDS – Compute Absent Words in Genomic Sequences

UNWORDS

:: DESCRIPTION

UNWORDS is an efficient software for computing shortest strings which do not occur in a given set of DNA sequences. UNWORDS is more efficient than previous algorithms and easier to use. It uses bit vector encoding of strings and therefore we called it unwords-bits. It directly computes unwords without the need to specify a length estimate. Moreover, it avoids the space requirements of index structures such as suffix trees and suffix arrays.

::DEVELOPER

Stefan Kurtz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

UNWORDS Source Code

:: MORE INFORMATION

Citation

Herold, J. and Kurtz, S. and Giegerich, R.
Efficient Computation of Absent Words in Genomic Sequences,
BMC Bioinformatics, 2008, 9:167.

SPALN 2.2.1 – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence

SPALN 2.2.1

:: 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.

SPALN Online Version

::DEVELOPER

Osamu Gotoh

:: 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).

Riboswitch Scanner – pHMM based application for Detecting Riboswitches from Genomic Sequences

Riboswitch Scanner

:: DESCRIPTION

Riboswitch Scanner is a new web application which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity.

::DEVELOPER

Riboswitch Scanner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Riboswitch Scanner: An efficient pHMM-based web-server to detect riboswitches in genomic sequences.
Mukherjee S, Sengupta S.
Bioinformatics. 2015 Oct 30. pii: btv640.

DELIMINATE – Method for Loss-less Compression of Genomic Sequences

DELIMINATE

:: DESCRIPTION

DELIMINATE is a novel compression algorithm that can rapidly compress genomic sequence data in a loss-less fashion.

::DEVELOPER

Bio-Sciences R&D Division, TCS Innovation Labs

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • 7-zip compression package

:: DOWNLOAD

 DELIMINATE

:: MORE INFORMATION

Citation

DELIMINATE – A fast and efficient method for loss-less compression of genomic sequences
Mohammed, M.H., Dutta, A., Bose, T., Chadaram, S., and Mande, S.S.
Bioinformatics. 2012 Oct 1;28(19):2527-9

Qualiseq 20150216 – Quality Genomic Sequence Retrieval

Qualiseq 20150216

:: DESCRIPTION

QualiSeq is a Quality Genomic Sequence Retrieval Tool.

::DEVELOPER

Qualiseq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yu-Chang Cheng, Tz-Chao Lin, Kuo-His Lee, Yan-Hau Chen, Ming-Fang Tsai, Yi-Jung Lin, and Adam Yao (2006)
Qualiseq: Quality Genomic Sequence Retrieval,
Journal of Genetics and Molecular Biology Vol. 17, No. 4, 204-210, December 1, 2006

fragrep 2 – Efficient Search for Fragmented Patterns in RNA

fragrep 2

:: DESCRIPTION

fragrep implements an efficient algorithm for detecting nucleotide pattern fragments in genomes that occur in a given order. For each pattern a tolerance can be specified separately.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 fragrep

:: MORE INFORMATION

Citation

Axel Mosig, Julian Chen, Peter F. Stadler,
Homology Search with Fragmented Nucleic Acid Sequence Patterns,
Proc. Worksh. Alg. Bioinf. (WABI), 2007.

VIRGO 1.0 – Visualization of A-to-I RNA Editing Sites in Genomic Sequences

VIRGO 1.0

:: DESCRIPTION

Virgo is a tool for identifying A-to-I RNA Editing sites in human genomic sequences. Once you submit DNA sequences, VIRGO will analyze them and will highlight putative A-to-I RNA Editing sites.

::DEVELOPER

VIRGO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 7:S5. doi: 10.1186/1471-2105-14-S7-S5. Epub 2013 Apr 22.
VIRGO: visualization of A-to-I RNA editing sites in genomic sequences.
Distefano R1, Nigita G, Macca V, Laganà A, Giugno R, Pulvirenti A, Ferro A.