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some bioinformatics softwares   

2010-04-06 11:55:44|  分类: Bioinformatics |  标签: |举报 |字号 订阅

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Software

Our software packages are divided into the following categories:

Sequencing/Assembly

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

AMOS

Manipulation of input and output files related to whole-genome shotgun assembly. Currently maintained at CBCB at the University of Maryland.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Celera Assembler

Celera Assembler can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Elvira

High throughput assembly of amplicon reads for virus-sized genomes.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

JCVI Primer Designer

High throughput PCR primer design software.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Lucy

A tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

TIGR Assembler

Enabled the first published whole-genome assembly of a free-living organism in 1995. Last revised in 2003.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

TIGR SSS

Middleware for organizing large chunks of data to free the client from having to encode data storage specifics.

Gene Finding

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Glimmer

A microbial gene-finding system, especially in bacteria, archaea, and viruses. Currently maintained at CBCB at the University of Maryland.

Annotation

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

AAT

A tool for analyzing and annotating eukaryotic genomic sequences.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Manatee

Web-based gene evaluation and genome annotation tool to view, modify, and store annotation for prokaryotic and eukaryotic genomes.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

PASA

A eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structure...

Genome Analysis

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

DAGchainer

The DAGchainer software computes chains of syntenic genes found within complete genome sequences.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

k-mer Tools

DNA sequence analysis tools including ESTmapper, Snapper (for mapping reads), and ATAC (for aligning genomes).

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

MUMmer

MUMmer is a system for rapidly aligning entire genomes (draft or complete). Currently maintained at CBCB at the University of Maryland.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Pathema

A NIAID Bioinformatics Resource Center (BRC) containing in depth curatorial analysis of six target organisms from the list of NIAID category...

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

PhageFinder

A tool to identify prophage regions within bacterial genomes.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Sybil

Sybil is a web-based software package for comparative genomics.

Microarray Tools

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Ginkgo

Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis and normalization package.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

Magnolia

Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

SNP Filter Scripts

Scripts to identify and filter out false positive SNP calls that are present in raw data from Affymetrix GeneChip® resequencing arrays.

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

TM4

TM4 is a suite of open source software tools that manage and analyze data from microarray experiments.

Proteomics Tools

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

APEX

The APEX tool is an implementation of the Absolute Protein Expression quantitation technique, computing protein abundance values for LC-MS/M...

Cloud

some bioinformatics softwares  - xiaofeng1982 - Tiger-Leon

JCVI Cloud BioLinux

Enabling scientists to quickly provision cloud-based bioinformatics platforms such as Amazon EC2 and Eucalyptus.

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