RSS 14 projects tagged "Bioinformatics"

Download Website Updated 27 Sep 2009 Bioperl

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Pop 98.85
Vit 8.03

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

No download Website Updated 15 Aug 2001 Ensembl

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Pop 18.28
Vit 1.83

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

Download Website Updated 02 Mar 2001 PDBCat

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Pop 18.28
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 19 Feb 2002 SLRI Bioinformatics Workshop

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Pop 10.44
Vit 66.69

The Samuel Lunenfeld Research Institute (SLRI) Bioinformatics Toolkit is a mainly C-based cross-platform toolkit for dealing with biological information, especially protein structure/function information. It is based on the NCBI Toolkit.

Download Website Updated 15 Sep 2003 Shrubberies - Linux Command Line Viewer

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Pop 13.93
Vit 2.39

slcview allows you to fully script creation of clustergrams and tree diagrams from .cdt, .gtr, and .atr files as output by several biologically-oriented clustering programs, namely Cluster and XCluster. Many options allow you control of the output, and, in addition, slcview allows you to create an annotated legend with the same scale of colors as used in your clustergram.

Download Website Updated 07 Nov 2002 Multi-Genome Navigator

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Pop 10.95
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 No website Updated 05 Aug 2003 run_mpiBLAST

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Pop 14.14
Vit 1.00

run_mpiblast makes running mpiBLAST on a cluster in the presence of other users, and queuing systems somewhat more robust. It allows users to catch errors in configuration well in advance of the actual execution, and allows them to submit the run to a queuing system.

No download Website Updated 23 Feb 2011 Berkeley DB XML

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Pop 123.17
Vit 3.11

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 Website Updated 29 Dec 2004 Genome-Tools

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Pop 22.18
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.

No download Website Updated 18 Oct 2006 PerlPrimer

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Pop 33.91
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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