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NAR Web Server Issue 2004

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Found 123 links

Displaying 15 links

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AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/ [open in a new window]

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DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
AGenDA: gene prediction by cross-species sequence comparison200411
NAR Web Server Issue 2004
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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

ArrayPipeTool Content

http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl [open in a new window]

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Expression > Transcript Expression Analysis

ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.

links directory index: 59
TitlePublication YearGoogle Scholar Citation Count
ArrayPipe: a flexible processing pipeline for microarray data200459
NAR Web Server Issue 2004
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ArrayProspectorTool Content

http://string32.embl-heidelberg.de:8080/prophecies_html/prophecies.html [open in a new window]

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Expression > Transcript Expression Analysis

ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
ArrayProspector: a web resource of functional associations inferred from microarray expression data200421
NAR Web Server Issue 2004
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tagsalgorithms animals gene expression profiling humans oligonucleotide array sequence analysis proteins reproducibility of results

ArrayXPathTool Content

http://www.snubi.org/software/ArrayXPath/ [open in a new window]

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Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.

links directory index: 111
TitlePublication YearGoogle Scholar Citation Count
ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics200543
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics200468
NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagscluster analysis gene expression profiling genetic databases genetic predisposition to disease medical subject headings oligonucleotide array sequence analysis signal transduction statistical data interpretation systems integration

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/ [open in a new window]

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Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences200424
NAR Web Server Issue 2004
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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus [open in a new window]

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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.

links directory index: 233
TitlePublication YearGoogle Scholar Citation Count
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources200687
AUGUSTUS: ab initio prediction of alternative transcripts200650
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints200534
AUGUSTUS: a web server for gene finding in eukaryotes200461
The formation of deoxycholic acid in patients with type II and IV hyperlipoproteinaemia19761
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

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
BEARR: Batch Extraction and Analysis of cis-Regulatory Regions200415
NAR Web Server Issue 2004
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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Molecular Dynamics and Docking
Protein > Networks & Interactions, Pathways and Enzymes

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
BioInfo3D: a suite of tools for structural bioinformatics200424
NAR Web Server Issue 2004
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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

links directory index: 702
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes2001670
NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/ [open in a new window]

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DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching and Classification

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

links directory index: 41787
TitlePublication YearGoogle Scholar Citation Count
NCBI BLAST: a better web interface2008167
BLAST: improvements for better sequence analysis2006101
BLAST: at the core of a powerful and diverse set of sequence analysis tools2004556
Basic local alignment search tool199040963
NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
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external linksLink on Wikipedia
setsNational Center for Biotechnology Information (NCBI)

BOMPTool Content

http://www.bioinfo.no/tools/bomp [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Localization and Targeting

The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.

links directory index: 85
TitlePublication YearGoogle Scholar Citation Count
BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria200485
NAR Web Server Issue 2004
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tagsbacterial genome bacterial outer membrane proteins escherichia coli gram-negative bacteria protein sequence analysis salmonella typhimurium secondary protein structure

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BSDD: Biomolecules Segment Display Device--a web-based interactive display tool20041
NAR Web Server Issue 2004
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tagsamino acid motifs molecular models molecular structure proteins

CARNACTool Content

http://bioinfo.lifl.fr/carnac [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.

links directory index: 130
TitlePublication YearGoogle Scholar Citation Count
CARNAC: folding families of related RNAs200467
Finding the common structure shared by two homologous RNAs200363
NAR Web Server Issue 2004
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CARRIETool Content

http://zlab.bu.edu/CARRIE-web [open in a new window]

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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.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis200430
Questions and answers about AIDS.19920
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

CaspRTool Content

http://igs-server.cnrs-mrs.fr/Caspr/index.cgi [open in a new window]

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Protein > 3-D Structure Prediction

CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.

links directory index: 71
TitlePublication YearGoogle Scholar Citation Count
CaspR: a web server for automated molecular replacement using homology modelling200471
NAR Web Server Issue 2004
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