Spaced Words – Alignment-free Sequence Comparison

Spaced Words

:: DESCRIPTION

Spaced Words is a new approach to alignment-free sequence comparison. While most alignment-free algorithms compare the word-composition of sequences, Spaced Words uses a pattern of care and don’t care positions.

::DEVELOPER

Department of Bioinformatics , University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Spaced Words

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 3.
Fast alignment-free sequence comparison using spaced-word frequencies.
Leimeister CA1, Boden M, Horwege S, Lindner S, Morgenstern B.

D2NGS – Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads

D2NGS

:: DESCRIPTION

D2NGS is a C++ package which is intended to implement a program for the alignment-free comparison of genome sequences using NGS data using d2, d2* and d2S.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Compiler

:: DOWNLOAD

D2NGS

:: MORE INFORMATION

Citation

Song K, Ren J, Zhai ZY, Liu XM, Deng MH, and Sun FZ (2012)
Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract
Research in Computational Molecular Biology, 272-285.

multiAlignFree 1.0 – Multiple Alignment-Free Sequence Comparison

multiAlignFree 1.0

:: DESCRIPTION

multiAlignFree is an R package which intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

multiAlignFree

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2690-8. doi: 10.1093/bioinformatics/btt462. Epub 2013 Aug 29.
Multiple alignment-free sequence comparison.
Ren J1, Song K, Sun F, Deng M, Reinert G.

FASTA 36.3.8h – Sequence Comparison

FASTA 36.3.8h

:: DESCRIPTION

FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

::DEVELOPER

William R. Pearson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /Mac OsX / Windows

:: DOWNLOAD

FASTA

:: MORE INFORMATION

Citation:

Pearson WR, Lipman DJ.
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8.

Alfresco 0.94 – FRont-End for Sequence COmparison

Alfresco 0.94

:: DESCRIPTION

Alfresco‘s ( (FRont-End for Sequence COmparison) ) aim is to develop a new visualisation tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualised and used to find corresponding sequence domains.

::DEVELOPER

Niclas Jareborg

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Windows
Java

:: DOWNLOAD

Alfresco

:: MORE INFORMATION

Citation

Alfresco–a workbench for comparative genomic sequence analysis.
Jareborg N, Durbin R.
Genome Res. 2000 Aug;10(8):1148-57.

kmacs – the k Mismatch Average Common Substring Approach to Alignment-free Sequence Comparison

kmacs

:: DESCRIPTION

kmacs is a new approach to alignment-free sequence comparison. While most alignment-free methods rely on exact word matches, kmacs uses a distance measure based on inexact substing matches.

::DEVELOPER

Department of Bioinformatics , University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

kmacs

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 13. pii: btu331. [Epub ahead of print]
kmacs: the k-Mismatch Average Common Substring Approach to alignment-free sequence comparison.
Leimeister CA1, Morgenstern B2.

AnABlast – Detect potential Coding Regions in DNA by Sequence Comparison

AnABlast

:: DESCRIPTION

AnABlast is an algorithm to discover signals of protein-coding sequences within genomic regions. You can analyze a short nucleotide sequence (up to 25Kb in length or up to 1Mb if you upload the Blast report). It highlights genomic regions with stacked non-significant alignments (protomotifs) which would represent present or ancient protein-coding sequences. It allows to discover new genes in bacteria or exons in eukaryotic organisms.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Methods Mol Biol. 2019;1962:207-214. doi: 10.1007/978-1-4939-9173-0_12.
AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions.
Rubio A, Casimiro-Soriguer CS, Mier P, Andrade-Navarro MA, Garzón A, Jimenez J, Pérez-Pulido AJ

LAST r992 – Genome-Scale Sequence Comparison

LAST r992

:: DESCRIPTION

LAST enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.LAST is similar to BLAST, but it copes better with giga-scale biological sequences. It can also use sequence quality data, and it can indicate the ambiguity of each column in an alignment.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler

:: DOWNLOAD

LAST

:: MORE INFORMATION

Citation

Adaptive seeds tame genomic sequence comparison.
SM Kielbasa, R Wan, K Sato, P Horton, MC Frith,
Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110

PASH 3.0.6.2 – Large-scale Sequence Comparison Method

PASH 3.0.6.2

:: DESCRIPTION

PASH is an efficient large-scale sequence comparison method that uses positional hashing.

::DEVELOPER

Bioinformatics Research Laboratory, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
C++ Compiler

:: DOWNLOAD

PASH

:: MORE INFORMATION

Citation

Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A.
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
BMC Bioinformatics. 2010 Nov 23;11:572