RSS 14 projects tagged "Bioinformatics"

No download Website Updated 23 Feb 2011 Berkeley DB XML

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Pop 123.00
Vit 3.12

Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.

Download No website Updated 24 Feb 2011 Bioinformatics Benchmark System

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Pop 27.75
Vit 1.00

The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems. It is not trying to be the last word in informatics benchmarking, as there are simply too many codes, tests, data sets, and databases. The goal is to create a core of tests that all may download and use to probe specific elements of system performance. The end goal is to enable a pluggable set of tests, including the core tests, so that performance data may be gathered.

Download Website Updated 27 Sep 2009 Bioperl

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Pop 98.07
Vit 8.04

Bioperl is set of Perl Modules for bioinformatics. It contains objects for Sequences, features on Sequences, and other important bioinformatics attributes.

Download Website Updated 28 Mar 2007 ESTScan

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Pop 14.70
Vit 1.42

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. It is not a gene prediction program, nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity.

No download Website Updated 15 Aug 2001 Ensembl

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Pop 18.06
Vit 1.83

Ensembl is an open source project to create and automatically maintain annotations on DNA sequence.

Download Website Updated 09 Jul 2005 Fasta2SVG

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Pop 10.20
Vit 1.00

Fasta2SVG is a script that converts a fasta file containing a genomic DNA or protein sequence into an SVG vector graphic. It offers different modes for formatting alignments or simple sequences and various parameters such as color and size, which can be set on the command line.

Download Website Updated 29 Dec 2004 Genome-Tools

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Pop 22.32
Vit 1.49

Genome-Tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. A CGI-based Web interface is also available.

Download Website Updated 07 Nov 2002 Multi-Genome Navigator

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Pop 10.77
Vit 1.00

MuGeN is a package for interactively exploring multiple annotated genomes simultaneously, possibly mixed with computational analysis results. Map information can be loaded from various sources, and resulting images can be exported in different formats. Both an interactive GUI based environment and a batch mode program are provided.

Download Website Updated 02 Mar 2001 PDBCat

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Pop 18.11
Vit 1.00

PDBCat can be used to manipulate and process PDB files using commonly available text-processing tools such as Perl, awk, etc. The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column-based format which is designed to be read easily read by FORTRAN programs. PDBCat converts the ATOM and HETATM records of PDB files from this column-based format to a field-based one that is more easily processed by standard Unix tools.

No download Website Updated 18 Oct 2006 PerlPrimer

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Pop 33.47
Vit 4.84

PerlPrimer is a GUI application that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR), and sequencing. It aims to automate and simplify the process of primer design. Current features include calculation of possible primer-dimers, retrieval of genomic or CDNA sequences from Ensembl (including both sequences automatically for QPCR), the ability to BLAST search primers using the NCBI server, ORF, and CpG island detection algorithms, the ability to add cloning sequences to primers, automatically adjusted to be in-frame, and QPCR primer design without manual intron-exon boundary entry.

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