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Links tagged with 'base sequence'

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Found 109 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

AREsiteDatabase Content

http://rna.tbi.univie.ac.at/AREsite [open in a new window]

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RNA > Databases

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
AREsite: a database for the comprehensive investigation of AU-rich elements201113
NAR Database Issue 2011
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external linksLink on Wikipedia
tags3' untranslated regions adenine animals base sequence conserved sequence genomics humans mice nucleic acid databases rna sequence analysis rna-binding proteins sequence alignment uracil

ASePCRTool Content

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

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DNA > Tools For the Bench
Expression > Splicing

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs200510
NAR Web Server Issue 2005
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tagsalgorithms alternative splicing animals base sequence expressed sequence tags humans messenger rna mice molecular sequence data rats reverse transcriptase polymerase chain reaction tissue distribution

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

Berkeley Drosophila Genome ProjectResource Content

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

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Model Organisms > Fly

Good entrez to fly genome resources.

links directory index: 370
TitlePublication YearGoogle Scholar Citation Count
The Drosophila melanogaster genome200375
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes2002147
A Drosophila full-length cDNA resource2002148
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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

BioDASResource Content

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

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Computer Related > Bio-* Programming Tools

This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data.

links directory index: 384
TitlePublication YearGoogle Scholar Citation Count
The distributed annotation system2001384
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tagsbase sequence computational biology computer terminals genetic databases human genome humans reference values
setsOpen Bioinformatics Foundation

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

BWATool Content

http://bio-bwa.sourceforge.net/ [open in a new window]

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DNA > DNA and Genomic Analysis
Sequence Comparison > Other Alignment Tools

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.

links directory index: 1676
TitlePublication YearGoogle Scholar Citation Count
Fast and accurate long-read alignment with Burrows-Wheeler transform2010838
Fast and accurate short read alignment with Burrows-Wheeler transform2009838
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tagsalgorithms base sequence dna sequence analysis genomics human genome humans sequence alignment

BWT-SWTool Content

http://i.cs.hku.hk/~ckwong3/bwtsw/ [open in a new window]

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DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching and Classification

BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments (see BLAST Sensitivity), BWT-SW finds all local alignments.

links directory index: 47
TitlePublication YearGoogle Scholar Citation Count
Compressed indexing and local alignment of DNA200847
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tagsalgorithms base sequence chromosome mapping data compression dna dna sequence analysis human genome humans molecular sequence data sequence alignment

CNVerTool Content

http://compbio.cs.toronto.edu/cnver/ [open in a new window]

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Human Genome > Sequence Polymorphisms
Sequence Comparison > Pairwise Sequence Alignments

CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Detecting copy number variation with mated short reads201023
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tagsalgorithms base pairing base sequence chromosome breakage chromosome mapping dna copy number variations dna mutational analysis dna shuffling high-throughput nucleotide sequencing humans reproducibility of results
setsUniversity of Toronto

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

DCODE.ORGResource Content

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

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Human Genome > Other Resources
Sequence Comparison > Comparative Genomics

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
Dcode.org anthology of comparative genomic tools200532
NAR Web Server Issue 2005
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tagsbase sequence binding sites computational biology gene expression regulation genetic promoter regions genomics humans molecular evolution nucleic acid regulatory sequences phylogeny sequence alignment transcription factors

Defining Transcriptional Programs in Vascular EndotheliumResource Content

http://www.vessels.bwh.harvard.edu/ [open in a new window]

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Expression > Gene Regulation
Expression > Transcript Expression Analysis

This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.

links directory index: 398
TitlePublication YearGoogle Scholar Citation Count
Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation200426
Biomechanical activation of vascular endothelium as a determinant of its functional phenotype2001355
Argus--a new database system for Web-based analysis of multiple microarray data sets200117
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tagsbase sequence biomechanics complementary dna cultured cells dna primers factual databases gene expression profiling humans molecular sequence data nucleic acid hybridization oligonucleotide array sequence analysis phenotype reproducibility of results statistics as topic vascular endothelium

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt [open in a new window]

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DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

links directory index: 944
TitlePublication YearGoogle Scholar Citation Count
DINAMelt web server for nucleic acid melting prediction2005378
Prediction of hybridization and melting for double-stranded nucleic acids2004129
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding1994437
NAR Web Server Issue 2005
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tagsalgorithms animals bacterial rna base sequence calorimetry dna dna sequence analysis fungal rna genetic hybridization introns molecular sequence data nucleic acid conformation nucleic acid denaturation nucleic acid hybridization oligonucleotides oligoribonucleotides phylogeny rats rna rna sequence analysis single-stranded dna structure-activity relationship temperature theoretical models transition temperature

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