Tag: Local

SRAssembler v1.0.0 – Selective and Recursive local Assembler

SRAssembler v1.0.0

:: DESCRIPTION

SRAssembler is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologous to a query DNA or protein sequence.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SRAssembler

:: MORE INFORMATION

Citation

McCarthy TW, Chou HC, Brendel VP.
SRAssembler: Selective Recursive local Assembly of homologous genomic regions.
BMC Bioinformatics. 2019 Jul 2;20(1):371. doi: 10.1186/s12859-019-2949-4. PMID: 31266441; PMCID: PMC6604332.

PLAST v2.3.1 – Parallel Local Alignment Search Tool for Database Comparison

PLAST v2.3.1

:: DESCRIPTION

PLAST (Parallel Local Alignment Search Tool for Database Comparison) is an intensive bank sequence comparison with a parallel version of BLAST-like software.The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy.

::DEVELOPER

PLAST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac / Linux

:: DOWNLOAD

 PLAST

:: MORE INFORMATION

Citation

V.H. Nguyen, D. Lavenier,
PLAST: parallel local alignment search tool for database comparison,
BMC Bioinformatics, 2009 10(329).

Stellar 1.4.11 – Local Pairwise Aligner

Stellar 1.4.11

:: DESCRIPTION

STELLAR (SwifT Exact LocaL AligneR)  is a local pairwise aligner  that has full sensitivity, i.e. guarantees to report all matches of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. For filtering it applies the SWIFT algorithm, for which we have developed a new, exact verification strategy. STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments in the edit or hamming distance model.

::DEVELOPER

Stellar team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 Stellar

:: MORE INFORMATION

Citation

Kehr, B., Weese, D., Reinert, K. (2011).
STELLAR: fast and exact local alignments.
BMC Bioinformatics, 12(Suppl 9):S15, 2011.

LHiSA 20080507 – Local High-scoring Segments for Association

LHiSA 20080507

:: DESCRIPTION

LHiSA is an algorithm dedicated to large-scale association studies which aims to identify segments of genome involved in a disease. It is based on Local Score statistic and an automatic selection of the significant segments.

::DEVELOPER

SSB group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C++ Compiler / R package

:: DOWNLOAD

 LHiSA

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2006;5:Article22. Epub 2006 Sep 17.
Detecting local high-scoring segments: a first-stage approach for genome-wide association studies.
Guedj M, Robelin D, Hoebeke M, Lamarine M, Wojcik J, Nuel G.

laSV 1.0.2 – Local Assembly based Structural Variation Discovery tool

laSV 1.0.2

:: DESCRIPTION

laSV is a software that employs a local de novo assembly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets.

::DEVELOPER

ZLab, University of Massachusetts Medical School, Worcester, MA, USA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 laSV

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Sep 30;43(17):8146-56. doi: 10.1093/nar/gkv831. Epub 2015 Aug 17.
Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.
Zhuang J, Weng Z

AlignNemo 1.1 – Local Network Alignment method to integrate Homology and Topology

AlignNemo 1.1

:: DESCRIPTION

 AlignNemo (Aligning Network Modules), is a novel algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that related in sequence and topology. The subnetworks have a general topology and need not to correspond to specific interaction patterns thus more closely fit the models of functional complexes proposed in the literature.

::DEVELOPER

AlignNemo Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 AlignNemo

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e38107. Epub 2012 Jun 12.
AlignNemo: a local network alignment method to integrate homology and topology.
Ciriello G, Mina M, Guzzi PH, Cannataro M, Guerra C.

SequenceServer 2.0.0.rc8 – Set up a Local BLAST Web Server to Search & Share Sequence data

SequenceServer 2.0.0.rc8

:: DESCRIPTION

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

::DEVELOPER

Wurm Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SequenceServer

:: MORE INFORMATION

Citation

Sequenceserver: a modern graphical user interface for custom BLAST databases
Anurag Priyam, Ben J Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, Yannick Wurm
doi: http://dx.doi.org/10.1101/033142

Rnall 2.0 – RNA Local Secondary Structure Prediction

Rnall 2.0

:: DESCRIPTION

Rnall (RNA Local secondary structure prediction by Local symmetric mapping) predicts local RNA secondary structures for multiple sequences in the Fasta format or scans local secondary structure of a single genomic sequence in the Fasta format. Rnall scans the RNA sequence with a sliding window and extracts all LSS with sizes no longer than a window size using dynamic programming. Rnall has various potential applications, such as local secondary structure prediction in RNA molecules and RNA motif prediction (such as rho-independent/intrinsic terminator, riboswitch, siRNA, and viral RNA motifs).

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

Rnall

:: MORE INFORMATION

Citation

Wan, X.-F., G. Lin, and D. Xu. 2006.
Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes.
Journal of Bioinformatics and Computational Biology, 4(5):1015-31.

LocHap 2.0 – Local-Haplotype Variant Calling Software

LocHap 2.0

:: DESCRIPTION

LocHap is an ultra-fast computational pipeline for calling local haplotype variant using deep DNA-sequencing data to reveal cellular heterogeneity and somatic mosaicism.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 LocHap

:: MORE INFORMATION

Citation

Sengupta S, Gulukota K, Zhu Y, Ober C, Naughton K, Wentworth-Sheilds W, Ji Y.
Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples.
Nucleic Acids Res. 2016 Feb 18;44(3):e25. doi: 10.1093/nar/gkv953. Epub 2015 Sep 29. PMID: 26420835; PMCID: PMC4756850.

PROPOSAL – PROtein Comparison through Probabilistic Optimal Structure local ALignment

PROPOSAL

:: DESCRIPTION

PROPOSAL is a Gibbs sampling algorithm for multiple local alignment of 3D protein structures. PROPOSAL can produce biologically significant alignments in reasonable running time, even for large input instances.

::DEVELOPER

Giovanni Micale

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

  PROPOSAL

:: MORE INFORMATION

Citation:

Proteins comparison through probabilistic optimal structure local alignment.
Micale G, Pulvirenti A, Giugno R, Ferro A.
Front Genet. 2014 Sep 2;5:302. doi: 10.3389/fgene.2014.00302.