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Links tagged with 'algorithms'

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Found 370 links

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3D-FunTool Content

http://3dfun.bioinfo.pl [open in a new window]

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Protein > 3-D Structure Comparison
Protein > Annotation and Function

3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
3D-Fun: predicting enzyme function from structure20086
NAR Web Server Issue 2008
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tagsalgorithms enzymes molecular models protein structural homology

3D-JuryTool Content

http://meta.bioinfo.pl/submit_wizard.pl [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

links directory index: 775
TitlePublication YearGoogle Scholar Citation Count
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure2003115
3D-Jury: a simple approach to improve protein structure predictions2003592
Detection of reliable and unexpected protein fold predictions using 3D-Jury200368
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology computer simulation database management systems humans molecular models protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment tertiary protein structure

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html [open in a new window]

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Protein > 3-D Structure Prediction

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.

links directory index: 1748
TitlePublication YearGoogle Scholar Citation Count
Enhanced genome annotation using structural profiles in the program 3D-PSSM20001568
CAFASP-1: critical assessment of fully automated structure prediction methods1999180
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome bacterial proteins computational biology factual databases flavoproteins integrases molecular models molecular sequence data mycoplasma open reading frames protein folding proteins proteome reproducibility of results retroviridae proteins ribonuclease h secondary protein structure sequence alignment solvents structure-activity relationship

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

ACELATool Content

http://www.nactem.ac.uk/acela/ [open in a new window]

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Literature > Text Mining and Semantics

The ACELA (ACcElerated Annotation) tool aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations.

This content is being maintained by pthompson.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
Accelerating the annotation of sparse named entities by dynamic sentence selection200810
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tagsaccelerated annotation algorithms annotation tool artificial intelligence automated pattern recognition bibliographic databases named entity annotation natural language processing terminology as topic text mining
setsUniversity of Manchester

ACLAMEDatabase Content

http://aclame.ulb.ac.be/ [open in a new window]

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DNA > Databases

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). Classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
ACLAME: a CLAssification of Mobile genetic Elements, update 2010201022
NAR Database Issue 2010
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tagsalgorithms bacterial genome bacteriophages computational biology genetic databases interspersed repetitive sequences nucleic acid databases nucleic acid repetitive sequences plasmids

AcromineTool Content

http://www.nactem.ac.uk/software/acromine/ [open in a new window]

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Literature > Text Mining and Semantics

Acromine is an tool that finds full forms of acronyms that appear in MEDLINE.

This content is being maintained by pthompson.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Building a high-quality sense inventory for improved abbreviation disambiguation201012
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tagsalgorithms automatic acronym expansion bibliographic databases cluster analysis computational biology dictionaries as topic medline natural language processing polymerase chain reaction reproducibility of results statistical models x-ray computed tomography
setsUniversity of Manchester

Acromine DisambiguatorTool Content

http://www.nactem.ac.uk/software/acromine_disambiguation/ [open in a new window]

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Literature > Text Mining and Semantics

Given a biomedical text, Acromine Disambiguator correctly predicts expanded full forms of acronoyms appearing in the text. As acronyms appearing in biomedical texts are often ambiguous, such a disambiguation process is important to ensure the correct interpretation of the text.

This content is being maintained by pthompson.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Building a high-quality sense inventory for improved abbreviation disambiguation201012
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tagsalgorithms automatic acronym disambiguation automatic acronym expansion bibliographic databases cluster analysis computational biology dictionaries as topic medline natural language processing polymerase chain reaction reproducibility of results statistical models x-ray computed tomography
setsUniversity of Manchester

ACTTool Content

http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php [open in a new window]

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Expression > Transcript Expression Analysis
Model Organisms > Plants

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

links directory index: 96
TitlePublication YearGoogle Scholar Citation Count
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis200696
NAR Web Server Issue 2006
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tagsalgorithms arabidopsis circadian rhythm gene expression profiling oligonucleotide array sequence analysis plant genes transcription factors

ADGOTool Content

http://www.btool.org/ADGO2 [open in a new window]

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Expression > Gene Set Analysis
Expression > cDNA, EST, SAGE

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
ADGO 2.0: interpreting microarray data and list of genes using composite annotations.20113
ADGO: analysis of differentially expressed gene sets using composite GO annotation200625
NAR Web Server Issue 2011
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tagsalgorithms animals biological models cell differentiation computer simulation documentation gene expression profiling genes humans mice molecular sequence annotation oligonucleotide array sequence analysis protein databases proteins rats t-lymphocytes

ALGGENTool Content

http://alggen.lsi.upc.es/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters200640
FibreHelix, a program for calculating the X-ray diffraction pattern of macromolecules with helical symmetry: application to DNA coiled coils20052
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences20036
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN2003107
PROMO: detection of known transcription regulatory elements using species-tailored searches2002121
NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

AlgPredTool Content

http://www.imtech.res.in/raghava/algpred/ [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.

This content is being maintained by raghavagps.

links directory index: 57
TitlePublication YearGoogle Scholar Citation Count
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes200657
NAR Web Server Issue 2006
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tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
AliasServer: a web server to handle multiple aliases used to refer to proteins200426
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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

Align-mTool Content

http://bioinformatics.vub.ac.be/software/software.html [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
Align-m--a new algorithm for multiple alignment of highly divergent sequences200481
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tagsalgorithms amino acid sequence amino acid sequence homology genetic variation molecular sequence data protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment

AMIC@Tool Content

http://bioalgo.iit.cnr.it/amica [open in a new window]

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Expression > Transcript Expression Analysis

The All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
AMIC@: All MIcroarray Clusterings @ once20089
NAR Web Server Issue 2008
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tagsalgorithms cluster analysis gene expression profiling oligonucleotide array sequence analysis

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