LocARNA 1.9.2.1 – Global and Local Alignment of RNA

LocARNA 1.9.2.1

:: DESCRIPTION

LocARNA is a package of tools for producing fast and high-quality pairwise and multiple alignment of RNA sequences. It uses a complex RNA energy model for simultaneous folding and sequence/structure alignment of the RNAs. LocARNA performs global, sequence local, or even structurally local alignment of the molecules.

::DEVELOPER

Bioinformatics Group
Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

LocARNA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Dec 31;15(1):6602. [Epub ahead of print]
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs.
Otto C, Möhl M, Heyne S, Amit M, Landau GM, Backofen R, Will S.

RNA. 2012 May;18(5):900-14. doi: 10.1261/rna.029041.111. Epub 2012 Mar 26.
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.
Will S1, Joshi T, Hofacker IL, Stadler PF, Backofen R.

Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen
In: Nucleic Acids Research, 2010, 38 Suppl, W373-7

LPCF – Local Protein Community Finder

LPCF

:: DESCRIPTION

LPCF allows the user to quickly find a high-quality community close to a queried protein in any network available from BioGRID or specified by the user.

::DEVELOPER

Computational Biology Laboratory – Boston University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

LPCF

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Sep 18;10:297. doi: 10.1186/1471-2105-10-297.
Finding local communities in protein networks.
Voevodski K, Teng SH, Xia Y.

LFM-Pro – Detection of Significant Local Structural Sites in Proteins

LFM-Pro

:: DESCRIPTION

LFM-Pro (Local Feature Mining in Proteins) is a framework for automatically discovering family specific local sites and the features associated with these sites.

::DEVELOPER

Sacan Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Matlab

:: DOWNLOAD

LFM-Pro

:: MORE INFORMATION

Citation

Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang.
LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins.
Bioinformatics, 23(6):709-716, 2007

alfy 1.5 – Alignment-Free local homologY

alfy 1.5

:: DESCRIPTION

alfy is a computer program for comparing one or more query DNA sequences to a set of subject sequences. For each query sequence the output consists of a list of intervals indicating the closest homologue among the set of subject sequences.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
C Compiler

:: DOWNLOAD

alfy

:: MORE INFORMATION

Citation

Alignment-free detection of local similarity among viral and bacterial genomes.
Domazet-Lošo M, Haubold B.
Bioinformatics. 2011 Jun 1;27(11):1466-72.

clasp 1.1 – Local Fragment Chainer using Sum-of-pair Gap Costs

clasp 1.1

:: DESCRIPTION

clasp is a fast and flexible fragment chainer that supports linear and sum-of-pair gap costs and uses highly time-efficient index structure, i.e., Johnson priority queues and range trees padded with Johnson priority queues. Chaining of short match fragments helps to quickly and accurately identify region of synteny that may not be found using common local alignment heuristics alone.

::DEVELOPER

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

clasp

:: MORE INFORMATION

Citation:

Algorithms Mol Biol. 2011 Mar 18;6:4.
Fast local fragment chaining using sum-of-pair gap costs.
Otto C, Hoffmann S, Gorodkin J, Stadler PF.

PersonalGenBank 200610 – Local Sequence Database

PersonalGenBank 200610

:: DESCRIPTION

PersonalGenBank is a database software maintaining sequences and sequence information in GenBank-format. Generally, the user downloads a large chunk of sequences from GenBank to the local computer and then imports these sequences into PersonalGenBank.

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

PersonalGenBank

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!