> Tag > Links tagged with 'sequence analysis'

Links tagged with 'sequence analysis'

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Found 32 links

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ArachnoServer 2.0Database Content

http://www.arachnoserver.org [open in a new window]

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Model Organisms > Databases
Protein > Databases

ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface.

This content is being maintained by glennfking.

links directory index: 29
TitlePublication YearGoogle Scholar Citation Count
ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures201113
ArachnoServer: a database of protein toxins from spiders200916
NAR Database Issue 2011
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tagsanimals protein databases proteins sequence analysis spider venoms spiders

ATIVSTool Content

http://influenza.nhri.org.tw/ATIVS/ [open in a new window]

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Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.

This content is being maintained by Jade.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
ATIVS: analytical tool for influenza virus surveillance20094
NAR Web Server Issue 2009
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tagsantigenic variation h3n2 subtype influenza a virus human influenza humans influenza virus hemagglutinin glycoproteins orthomyxoviridae population surveillance sequence analysis viral antibodies viral antigens

BAGETTool Content

http://archaea.u-psud.fr/bin/baget.dll [open in a new window]

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Model Organisms > Microbes

BAGET (Bacterial and Archaeal Gene Exploration Tool) is a web service designed to facilitate extraction of specific gene and protein sequences from completely determined prokaryotic genomes. Query results can be exported as a rich text format file for printing, archival or further analysis.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence20087
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tagsarchaea bacteria database management systems genetic databases proteome sequence analysis

DePIETool Content

http://biocore.unl.edu/primer/primerPI.html [open in a new window]

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DNA > Tools For the Bench
Protein > Networks & Interactions, Pathways and Enzymes

Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
DePIE: Designing Primers for Protein Interaction Experiments20034
NAR Web Server Issue 2003
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tagsdna primers nucleic acid databases nucleic acid denaturation polymerase chain reaction protein databases protein sorting signals proteins sequence analysis tertiary protein structure two-hybrid system techniques yeasts

DotterTool Content

http://sonnhammer.sbc.su.se/Dotter.html [open in a new window]

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Sequence Comparison > Pairwise Sequence Alignments

Dotter is a dot-matrix program with interactive greyscale rendering for genomic DNA and protein sequence analysis.

links directory index: 480
TitlePublication YearGoogle Scholar Citation Count
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis1995480
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tagsamino acid sequence amino acid sequence homology data display molecular sequence data nucleic acid sequence homology sequence analysis

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/ [open in a new window]

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Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

links directory index: 250
TitlePublication YearGoogle Scholar Citation Count
Web services at the European Bioinformatics Institute-2009200935
Web services at the European bioinformatics institute2007143
SOAP-based services provided by the European Bioinformatics Institute200554
Public web-based services from the European Bioinformatics Institute200418
NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

EMBL-EBI FrameworkTool Content

http://www.ebi.ac.uk/Tools/sss [open in a new window]

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Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.

links directory index: 53
TitlePublication YearGoogle Scholar Citation Count
A new bioinformatics analysis tools framework at EMBL-EBI201053
NAR Web Server Issue 2010
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tagscomputational biology nucleic acid databases protein databases sequence alignment sequence analysis

FANTOM - Functional Annotation of MouseDatabase Content

http://www.gsc.riken.go.jp/e/FANTOM/ [open in a new window]

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Model Organisms > Mouse and Rat

Functional annotations for RIKEN full-length cDNA clones.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Integrated analysis of the genome and the transcriptome by FANTOM20043
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tagsalgorithms animals chromosome mapping database management systems documentation genome mice phylogeny proteome sequence alignment sequence analysis systems integration transcription factors

GenDecoderTool Content

http://darwin.uvigo.es/software/gendecoder.html [open in a new window]

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DNA > Structure and Sequence Feature Detection
Sequence Comparison > Multiple Sequence Alignments

GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
GenDecoder: genetic code prediction for metazoan mitochondria200615
NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence codon conserved sequence mitochondrial genes molecular evolution protein biosynthesis sequence alignment sequence analysis

GeneCardsDatabase Content

http://www.genecards.org/ [open in a new window]

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Human Genome > Health and Disease

Database of human genes, their products, and involvement in diseases; free for non-commercial use, but users should also read the Terms of Use for this site.

links directory index: 124
TitlePublication YearGoogle Scholar Citation Count
GeneCards: integrating information about genes, proteins and diseases1997124
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external linksLink on Wikipedia
tagsalgorithms chromosome mapping computer communication networks database management systems factual databases gene expression profiling genetic databases human genome human genome project humans information storage and retrieval internet medical genetics sequence alignment sequence analysis software user-computer interface

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

links directory index: 714
TitlePublication YearGoogle Scholar Citation Count
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update20044
The web server of IBM's Bioinformatics and Pattern Discovery group20039
Dictionary-driven prokaryotic gene finding200241
Dictionary-driven protein annotation200237
The emergence of pattern discovery techniques in computational biology200092
Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes.19990
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm1998531
NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

INCLUSiveTool Content

http://www.esat.kuleuven.ac.be/inclusive [open in a new window]

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

INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis200349
NAR Web Server Issue 2003
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tagsalgorithms cluster analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis registries sequence analysis systems integration

Influenza Virus ResourcesResource Content

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

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Model Organisms > Other Organisms

Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.

links directory index: 498
TitlePublication YearGoogle Scholar Citation Count
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses2005222
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution2005276
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tagsanimals genetic recombination genetic variation genome h3n2 subtype influenza a virus human influenza humans influenza a virus influenza vaccines influenza virus hemagglutinin glycoproteins molecular evolution mutagenesis mutation neuraminidase new york phylogeny public sector reassortant viruses sequence analysis time factors viral genes viral genome virus replication

KAASTool Content

http://www.genome.jp/kegg/kaas/ [open in a new window]

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DNA > Annotations
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

links directory index: 168
TitlePublication YearGoogle Scholar Citation Count
KAAS: an automatic genome annotation and pathway reconstruction server2007168
NAR Web Server Issue 2007
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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

KOBASTool Content

http://kobas.cbi.pku.edu.cn [open in a new window]

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DNA > Annotations
Human Genome > Databases
Protein > Networks & Interactions, Pathways and Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

links directory index: 215
TitlePublication YearGoogle Scholar Citation Count
KOBAS server: a web-based platform for automated annotation and pathway identification200675
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary2005140
NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

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