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Links tagged with 'chromosomes'

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ChimerDBDatabase Content

http://ercsb.ewha.ac.kr/fusiongene [open in a new window]

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DNA > Databases

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChimerDB 2.0--a knowledgebase for fusion genes updated20106
NAR Database Issue 2010
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tagsalgorithms animals chromosomes computational biology expressed sequence tags gene expression profiling gene fusion genetic databases genetic translocation genomics humans information storage and retrieval internet messenger rna mice mutant chimeric proteins nucleic acid databases protein databases pubmed rats software user-computer interface

EMMADatabase Content

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

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Model Organisms > Databases

The European Mouse Mutant Archive (EMMA) is an infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resources (FIMRe), EMMA being the European component. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl.

This content is being maintained by damiansmedley.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
EMMA--mouse mutant resources for the international scientific community201014
NAR Database Issue 2010
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tagsanimals chromosomes computational biology genetic databases genetic models inbred c57bl mice knockout mice mice nucleic acid databases protein databases tertiary protein structure

FeatureExtractTool Content

http://www.cbs.dtu.dk/services/FeatureExtract/ [open in a new window]

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DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
FeatureExtract--extraction of sequence annotation made easy20058
NAR Web Server Issue 2005
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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp [open in a new window]

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Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
FGF: a web tool for Fishing Gene Family in a whole genome database20073
NAR Web Server Issue 2007
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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

LowComplexityTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
Complexity: an internet resource for analysis of DNA sequence complexity200449
NAR Web Server Issue 2004
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tagsalgorithms bacterial genome chromosomes dna sequence analysis sequence alignment

NGSmethDBDatabase Content

http://bioinfo2.ugr.es/NGSmethDB/gbrowse/ [open in a new window]

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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.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data20118
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

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