Nucleosee – Visual Genome-wide search of Nucleosome Patterns

Nucleosee

:: DESCRIPTION

Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Nucleosee

:: MORE INFORMATION

Citation

Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192

HaMStR 13.2.6 – Hidden Markov Model based Search for Orthologs using Reciprocit

HaMStR 13.2.6

:: DESCRIPTION

HaMStR (Hidden Markov Model based Search for Orthologs using Reciprocity)is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HaMStR

:: MORE INFORMATION

Citation:

BMC Evol Biol. 2009 Jul 8;9:157.
HaMStR: profile hidden markov model based search for orthologs in ESTs.
Ebersberger I, Strauss S, von Haeseler A.

GWFASTA – FASTA search in Eukaryotic and Microbial Genomes

GWFASTA

:: DESCRIPTION

GWFASTA (Genome Wise Sequence Similarity Search using FASTA) allows user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search

::DEVELOPER

GWFASTA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Issac, B. and Raghava, G. P. S.(2002)
GWFASTA: A server for FASTA search in Eukaryotic and Microbial genomes.
BioTechniques 33(3):548-556.

BlastR 2.2 – Searching and Clustering RNA

BlastR 2.2

:: DESCRIPTION

BlastR is a new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides. We have shown that this approach has better sensitivity and specifity than other softwares with comparable computational cost. BlastR package is a perl wrapper for BlastP and it is part of the T-Coffee distribution.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BlastR

:: MORE INFORMATION

Citation

Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.
BlastR—fast and accurate database searches for non-coding RNAs
Nucleic Acids Res. 2011 Sep 1;39(16):6886-95.

RNATOPS 1.2 – RNA Pseudoknot Search in Genomes

RNATOPS 1.2

:: DESCRIPTION

RNATOPS (RNA via Tree decOmPoSition) is a program that searches for RNA secondary structures based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Complier

:: DOWNLOAD

 RNATOPS

:: MORE INFORMATION

Citation

Huang, Z., Wu, Y., Robertson, J., Feng, L., Malmberg, R., and Cai, L. (2008)
Fast and accurate search for non-coding RNA pseudoknot structures in genomes,
Bioinforamtics, 24(20):2281-2287.

YASS 1.15 – Genomic Similarity Search Tool

YASS 1.15

:: DESCRIPTION

YASS  (Yet Another Similarity Searcher) is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments).  Like most of the heuristic DNA local alignment software (BLAST, FASTA, PATTERNHUNTER, BLASTZ …), YASS uses seeds to detect potential similarity regions, and then tries to extend them to actual alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step

YASS Online Version

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 YASS

:: MORE INFORMATION

Citation

L. Noe, G. Kucherov,
YASS: enhancing the sensitivity of DNA similarity search, 2005,
Nucleic Acids Research, 33(2):W540-W543.

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.

ExactSearch – A Fast Plant Motif Search Tool

ExactSearch

:: DESCRIPTION

ExactSearch is a web tool which enables plant biologists to search for DNA motifs in the proximal promoters, and 3′ untranslated regions of all genes from 50 genome-sequenced plant species.

::DEVELOPER

ExactSearch team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ExactSearch: a web-based plant motif search tool.
Gunasekara C, Subramanian A, Avvari JV, Li B, Chen S, Wei H.
Plant Methods. 2016 Apr 28;12:26. doi: 10.1186/s13007-016-0126-6.

SequenceServer 1.0.6 – Set up a Local BLAST Web Server to Search & Share Sequence data

SequenceServer 1.0.6

:: 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

CUDASW++ 3.1.1 – Parallel Smith Waterman Protein database search algorithm

CUDASW++ 3.1.1

:: DESCRIPTION

CUDASW++ (compute unified device architecture) is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA toolkits and SDK 2.0 or higher.

:: DOWNLOAD

 CUDASW++

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions“.
BMC Research Notes, 2010, 3:93