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Links tagged with 'female'

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AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

CARRIETool Content

http://zlab.bu.edu/CARRIE-web

Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.

NAR Web Server Issue 2004
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tagsacquired immunodeficiency syndrome binding sites computational biology dna female gene expression profiling gene expression regulation genetic promoter regions genetic transcription hiv hiv infections humans male newborn infant nucleic acid regulatory sequences nurses oligonucleotide array sequence analysis physicians pregnancy transcription factors

CCDBDatabase Content

http://crdd.osdd.net/raghava/ccdb

DNA > Databases

The Cervical Cancer gene DataBase (CCDB) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. Each record contains details related to gene like architecture (exon-intron structure), location, function, sequences (mRNA/CDS/protein), ontology, interacting partners, homology to other eukaryotic genomes, structure and links to other public databases, thus augmenting CCDB with external data. Also, manually curated literature references have been provided to support the inclusion of the gene in the database and establish its association with cervix cancer. In addition, CCDB provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search.

NAR Database Issue 2011
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tagsfemale genetic databases humans neoplasm genes uterine cervical neoplasms

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

NAR Web Server Issue 2007
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

GeSBAPTool Content

http://bioinfo.cipf.es/gesbap/

Expression > Gene Set Analysis
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.

NAR Web Server Issue 2009
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tagsbiological processes breast neoplasms female genes genetic variation genome-wide association study humans single nucleotide polymorphism

mirActTool Content

http://sysbio.ustc.edu.cn/software/mirAct

Expression > Transcript Expression Analysis
RNA > Functional RNAs

mirACT web server is a tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.

This content is being maintained by zhouzhou.

NAR Web Server Issue 2011
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tagsbreast neoplasms cluster analysis female gene expression humans micrornas

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2003NAR Web Server Issue 2006NAR Web Server Issue 2007
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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

PINTTool Content

http://csb2.ym.edu.tw/pint/

Expression > Gene Set Analysis
Protein > Interactions, Pathways, Enzymes

Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted.

NAR Web Server Issue 2010
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tagsbiological models breast neoplasms cyclin d erbb-2 receptor female humans rac gtp-binding proteins ras proteins signal transduction

SAGEmapDatabase Content

http://www.ncbi.nlm.nih.gov/SAGE/

Expression > cDNA, EST, SAGE

SAGE tag to gene mapping by NCBI.

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tagscomputer-assisted signal processing dna sequence analysis factual databases female gene expression gene library humans male sequence tagged sites
setsNational Center for Biotechnology Information (NCBI)