BioSoftwares

SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20–30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome.

OS: Linux

Licence: Freeware

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The biobar project is a bioinformatics power-browsing toolbar for Mozilla-based browsers. This toolbar provides access to major biological data resources. The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases. In addition to the browsing features, biobar also provides links to important bioinformatics sites and services including services at the European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ). The tool also provides links to major data deposition sites for nucleotide, protein and 3D-structure data. Finally, the menu also contains links to many Sequence, Structure alignment and analysis tools.

Covered Databases

# Data Collections

• EBI Databases with SRS
• NCBI Databases
• DNA Database of Japan(DDBj)

# Functional Databases

• aMAZE
• araCyc
• BioCyc
• KEGG
• Gene Ontology (GO)
• IntAct
• PRIDE
• PhenomicDB
• Reactome Database

# Sequence Databases

• EMBL Nucleotide Database
• Ensembl Genome Browser
• UniProt Sequence Database
• InterPro
• Integr8
• Expert Protein Analysis System (ExPASy)
• Pfam
• Alternative Splicing Database (ASD)

# Structural Databases

• Macromolecular Structure Database (MSD)
• Research Collaboratory for Structural Bioinformatics (RCSB)
• Protein Data Bank Japan (PDBj)
• BMRB
• OCA
• PDBsum
• EM-Search
• Nucleic Acid Database (NDB)
• CATH
• SCOP
• EDS

# Animal Databases

• Saccharomyces Genome Database (SGD)
• Flybase
• Wormbase
• Rat Genome Database (RGD)
• Mouse Genome Informatics (MGI)
• Zebrafish Information (ZFIN)

# Plant Databases

• Gramene
• GrainGenes
• MaizeGDB
• Tropicos

Browser: Firefox/Flock/Mozilla/Netscape and Seamonkey

Licence: Freeware

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Life Science Dictionary Tool is a Mouseover dictionary that can translate vast numbers of life science terms. 93,000 English terms and 105,000 Japanese terms available with examples and gene information collected from life science dictionary project.

Features

• Word dictionary – It will immediately pop up the meaning, related terms and example sentences when putting a mouse over the unknowing technical terms and names,
• Translates phrases! – Immediately translate phrases made with multiple words!
• Key combination – Translation operates only when holding down with selected key combination.
• Range selecting translation – When multiple numbers of phrases match, you can select one term and translate individually. Available when using key combination function.
• Change highlight color – You can change the highlight color of the matched term in the dictionary.

Browser: Mozilla Firefox

Licence: Freeware

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Wired-Marker is a permanent (indelible) highlighter that you use on Web pages. The highlighter, which comes in various colors and styles, is a kind of electronic bookmark that serves as a guide when you revisit a Web page. The highlighted content is automatically recorded in a scrapbook and saved.
Wired-Marker is a freeware that was developed as part of the Integrated Database Project sponsored by the Ministry of Education, Culture, Sports, Science and Technology (development code name: ScrapParty) for supporting the construction of databases.
Ministry of Education, Culture, Sports, Science and Technology (2006) Integrated Database Project “Integrated Database for Life Sciences” II-3 Technology Development for Curator Support.

Browser: Mozilla Firefox

Licence: Freeware

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