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Links tagged with 'male'

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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

Berkeley Drosophila Genome ProjectResource Content

http://www.fruitfly.org/

Model Organisms > Fly

Good entrez to fly genome resources.

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tagsamino acid sequence animals base sequence cell line cluster analysis complementary dna dna sequence analysis drosophila melanogaster expressed sequence tags gene library genetic databases genome insect genes male membrane glycoproteins membrane proteins molecular sequence data rna sequence alignment testis

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

CENTDISTTool Content

http://compbio.ddns.comp.nus.edu.sg/~chipseq/centdist/

Expression > Gene Regulation

CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks.

NAR Web Server Issue 2011
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tagsandrogen receptors binding sites chromatin immunoprecipitation dna sequence analysis humans male prostatic neoplasms transcription factors transcriptional regulatory elements tumor cell line

CONFACTool Content

http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl

Expression > Gene Regulation
Expression > Transcript Expression Analysis

The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.

NAR Web Server Issue 2004
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tagsanimals binding sites ccaat-enhancer-binding protein-delta ccaat-enhancer-binding proteins dna sequence analysis gene expression profiling genetic promoter regions genomics humans male mice nf-kappa b oligonucleotide array sequence analysis prostatic neoplasms transcription factors

DDPCDatabase Content

http://apps.sanbi.ac.za/ddpc/

DNA > Databases

Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC.

NAR Database Issue 2011
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tagsdata mining genetic databases humans knowledge bases male neoplasm genes prostatic 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

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)

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo

DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

NAR Web Server Issue 2009
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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors