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Links tagged with 'cpg islands'

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DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/

DNA > Tools For the Bench
Human Genome > Health and Disease

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

NAR Web Server Issue 2006
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tagscodon computational biology cpg islands dna primers dna vaccines drug design gene expression polymerase chain reaction restriction mapping systems integration

FirstEFTool Content

http://rulai.cshl.org/tools/FirstEF/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

First Exon Finder (FirstEF) is a 5\' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.

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tagscpg islands exons genetic promoter regions human chromosomes human genome humans

GC-ProfileTool Content

http://tubic.tju.edu.cn/GC-Profile/

DNA > Structure and Sequence Feature Detection

GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.

NAR Web Server Issue 2006
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tagsalgorithms animals archaeal genome automated pattern recognition bacterial genome base composition base sequence chickens chromosome mapping cpg islands cytosine dna dna sequence analysis genetic models genomic islands genomics guanine isochores molecular sequence data sequence alignment statistical models

IslandPathTool Content

http://www.pathogenomics.sfu.ca/islandpath/

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

IslandPath aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizontal origin.

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tagsarchaea archaeal genome bacteria bacterial genome cpg islands database management systems dna sequence analysis horizontal gene transfer phylogeny sequence alignment

NGSmethDBDatabase Content

http://bioinfo2.ugr.es/NGSmethDB/gbrowse/

DNA > Databases

NGSmethDB contains methylation data derived from next-generation sequencing (NGS). Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. NGSmethDB is currently populated with human, mouse and Arabidopsis data.

NAR Database Issue 2011
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tagsanimals chromosomes cpg islands cytosine data mining dna methylation dna sequence analysis genetic promoter regions genomics humans mice nucleic acid databases

QUMATool Content

http://quma.cdb.riken.jp/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. Users can also control the quality of aligned sequences by changing cutoff paramteres.

NAR Web Server Issue 2008
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tagscpg islands dna methylation dna sequence analysis statistical data interpretation sulfites