> Tag > Links tagged with 'nucleic acid sequence homology'

Links tagged with 'nucleic acid sequence homology'

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Found 45 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

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

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html [open in a new window]

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DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
BLASTO: a tool for searching orthologous groups200718
NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

CentroidHomfold-LASTTool Content

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

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RNA > Structure Prediction, Visualization, and Design

CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences20112
NAR Web Server Issue 2011
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tagsnucleic acid conformation nucleic acid sequence homology rna rna sequence analysis

CONREALTool Content

http://conreal.niob.knaw.nl/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

links directory index: 125
TitlePublication YearGoogle Scholar Citation Count
CONREAL web server: identification and visualization of conserved transcription factor binding sites200541
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting200484
NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

cpnDBDatabase Content

http://www.cpndb.ca/cpnDB/home.php [open in a new window]

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DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Data
Protein > Sequence Retrieval

cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
cpnDB: a chaperonin sequence database200473
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tagsanimals bacteria base sequence chaperonin 60 computational biology genetic databases molecular sequence data nucleic acid sequence homology

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

ERPINTool Content

http://tagc.univ-mrs.fr/erpin/ [open in a new window]

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RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

links directory index: 165
TitlePublication YearGoogle Scholar Citation Count
The ERPIN server: an interface to profile-based RNA motif identification200436
Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles2001129
NAR Web Server Issue 2004
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tagsalgorithms base sequence computational biology conserved sequence gene expression regulation iron nucleic acid conformation nucleic acid sequence homology response elements ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis selenocysteine sensitivity and specificity sequence alignment transfer rna

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences200337
NAR Web Server Issue 2003
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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

FASTA ProgramsTool Content

http://fasta.bioch.virginia.edu/ [open in a new window]

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Sequence Comparison > Similarity Searching and Classification

Sequence retrieval and comparison tools.

links directory index: 12295
TitlePublication YearGoogle Scholar Citation Count
Rapid and sensitive sequence comparison with FASTP and FASTA19901956
Improved tools for biological sequence comparison198810339
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tagsadrenergic receptors algorithms amino acid sequence animals antigen receptors base sequence dna eye proteins gene library globins humans information systems molecular sequence data nucleic acid sequence homology peptides proteins rod opsins transforming growth factors

HMMgeneTool Content

http://genome.cbs.dtu.dk/services/HMMgene/ [open in a new window]

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DNA > Gene Prediction

Prediction of vertebrate and C. elegans genes.

links directory index: 96
TitlePublication YearGoogle Scholar Citation Count
Using database matches with for HMMGene for automated gene detection in Drosophila200096
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tagsalcohol dehydrogenase animals computational biology computer-assisted numerical analysis drosophila melanogaster factual databases insect genes markov chains nucleic acid sequence homology sensitivity and specificity

INDELSCANTool Content

http://indelscan.genomics.sinica.edu.tw/IndelScan/ [open in a new window]

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DNA > Annotations
Sequence Comparison > Analysis of Aligned Sequences

INDELSCAN is a tool for genome-wide identification of indels.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events20072
NAR Web Server Issue 2007
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tagsanimals base sequence computational biology genetic polymorphism human genome humans molecular sequence data mutation nucleic acid sequence homology saccharomyces cerevisiae sequence deletion single nucleotide polymorphism species specificity

IPDDatabase Content

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

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Human Genome > Databases

The Immuno Polymorphism Database (IPD) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. IPD consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
IPD--the Immuno Polymorphism Database201030
NAR Database Issue 2010
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tagsalleles animals base sequence computational biology genetic databases genetic polymorphism humans immune system immunogenetics molecular sequence data nucleic acid databases nucleic acid sequence homology protein databases

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/ [open in a new window]

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DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
The ITS2 Database III--sequences and structures for phylogeny201038
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses200667
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures200559
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota2005112
NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

ITS2Database Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?search [open in a new window]

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DNA > Databases

The ITS2 Database holds information about sequence, structure and taxonomic classification of all internal transcribed spacer 2 (ITS2) in GenBank. ITS2 can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
The ITS2 Database III--sequences and structures for phylogeny201038
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
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external linksLink on Twitter
tagsbase sequence computational biology fungal genome fungi genetic databases molecular sequence data nucleic acid databases nucleic acid sequence homology plant genome plants ribosomal spacer dna tertiary protein structure

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