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The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer.

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• SciCrunch
• 17 years ago - by Anonymous

HepSEQ is the International Repository for Hepatitis B Virus Strain Data. It is web-accessible, quality-based, molecular, clinical and epidemiological database for hepatitis B infection and provides a tool for the research community or for those involved in hepatitis B case management. This database currently has 1012 patient records and 1253 viral sequences. The quality of all submitted sequences is checked. The tools provided include: SeqMatch: search the database for matching sequences Genotyper: genotype HBV strains (based on HBV surface antigen genes) Gene Mutation: display the sequences that contain mutations in HBV coding regions Mutation Annotator: annotate sequences for mutation known to be associated with anti-viral resistance This web database development is funded by the UK Department of Health is curated and is hosted by the Health Protection Agency.

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• SciCrunch
• 17 years ago - by Anonymous

Genomic database that includes prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The euHCVdb is a Hepatitis C Virus database oriented towards protein sequence, structure and function analyses and structural biology of HCV. In order to make the existing HCV databases as complementary as possible, the current developments are coordinated with the other databases (Japan and Los Alamos) as part of an international collaborative effort. It is monthly updated from the EMBL Nucleotide sequence database and maintained in a relational database management system. Programs for parsing the EMBL database flat files, annotating HCV entries, filling up and querying the database used SQL and Java programming languages. Great efforts have been made to develop a fully automatic annotation procedure thanks to a reference set of HCV complete annotated well-characterized genomes of various genotypes. This automatic procedure ensures standardization of nomenclature for all entries and provides genomic regions/proteins present in the entry, bibliographic reference, genotype, interesting sites or domains, source of the sequence and structural data that are available as protein 3D models. Hepatitis C, Hepatitis C Virus, Hepatitis C Virus protein .

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• SciCrunch
• 17 years ago - by Anonymous

Haptendb is a database of haptens which provide comprehensive information about the Hapten molecule, ways to raise antibodies against particular group of haptens, specificity and cross reactivity of raised antibody with related haptens, use of antibodies in constructing cost effective and simple detection kits. Major Features of the Database include: It covers wide array of haptens that includes; pesticides, herbicides, insecticides, drugs, vitamins, steroids, hormones, toxins, dyes, explosives, etc. The database contains 2021 entries for antibodies either raised against haptens or cross-reactivity of antibody raised against one Hapten with other related haptens. Every single record in the database contains detailed information about the Hapten, the carrier and the antibodies along with the assay methods and their sensitivity towards Hapten detection. The database provides information about 1087 haptens that includes: (i) common and chemical name of Hapten, (ii) molecular mass, physical and chemical properties, (iii) biological importance and the structure. Haptendb provides online web tools that allows users to retrieve and analyze the data that includes: (i) tools for searching database using keywords with many options and, (ii) browsing tool that allows the user to browse the database on Hapten name, carrier protein and antibody. The database has 2-D and 3-D structures of most of haptens in standard format based on information in literature. It also allows sketching structures online and searching of similar structures in database. One of the powerful tools in Haptendb is structure similarity search tool, which allows user to search similar structures.

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• SciCrunch
• 17 years ago - by Anonymous

HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.

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• SciCrunch
• 16 years ago - by Anonymous

Collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available.

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• SciCrunch
• 17 years ago - by Anonymous

It is a database of point mutations and short additions and deletions in the factor IX gene. The database attempts to offer a view of the spectrum of mutations causing haemophilia B that is as accurate as possible and this is helped by the fact that about 1/3 of all mutations have been detected as a result of full population studies. However, some bias cannot be completely avoided. Obviously there is an over-representation of severe haemophilia-causing mutations as these tend to be the first analysed and the most likely to come to notice. We also expect under-representation of double mutants as not all laboratories have done complete gene screens. Haemophilia B, Haemophilia B Mutation, IX, IX gene, IX gene mutation

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• SciCrunch
• 14 years ago - by Anonymous

GTOP is a database consists of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures. GTOP is built by the Laboratory of Gene-Product Informatics at the National Institute of Genetics. This research is supported by the Japan Science and Technology Corporation and Grants-in-Aid for Scientific Research (Genomes in category C) from the Ministry of Education, Science, Sports and Culture of Japan. We use the following methods: Prediction of 3D structure Sequence homology search of PDB, using REVERSE PSI-BLAST. Functional predictions (family classifications) Sequence homology search of Swiss-Prot, a well-annotated sequence database, with the use of BLAST. Other analytical methods We are also carrying out the following analyses: Motif Analysis(PROSITE) Family classification(Pfam) Prediction of transmembrane helix domains(SOSUI) Prediction of coiled-coil regions(Multicoil) Repetitive sequence analysis(RepAlign)

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• SciCrunch
• 17 years ago - by Anonymous

GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB2 is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. Computations were performed with the help of an indigenously developed and previously published software program QGRS Mapper. What is new in GRSDB2: The entire database has been built with a new and much improved version of QGRS Mapper program. It contains data from a large number of eukaryotic genes from several organisms in addition to human and mouse. The data model is different than the first version in that it is centered around Entrez Gene rather than solely GenBank/RefSeq nucleotide entries. The search module has been greatly enhanced. It is possible to search the database with Entrez Gene ID, Gene Name, Gene Symbols, Aliases, relevant Accession numbers and many other parameters like numbers of poly A signals and alternatively spliced products. Complex queries can also be performed. In addition, it is now possible to search the database with Gene Ontology terms. The list of genes matching the query can be sorted. The website also allows to manipulate the list to form sets of genes and perform further computations on these sets through a ''Workbench''. The Gene View, Data View and Graphic View for individual database entries have been significantly enhanced with several additional computational capabilities and links. The data can now be exported into Excel for further analysis. In addition, we have added a Sequence View which displays mapped G-quadruplexes in the context of pre-mRNA sequence. GRSDB2 replaces GRSDB at, http://bioinformatics.ramapo.edu/grsdb/index.php

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• SciCrunch
• 17 years ago - by Anonymous

Grain Genes is a genome database for Triticeae and Avena. It contains tools that allow users to browse graingenes, search the MySQL database, and view maps, genetic markers, gene expression and sequences.

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• SciCrunch
• 17 years ago - by Anonymous

Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3.

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• SciCrunch
• 13 years ago - by Anonymous

A database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. The objectives of the database are: Provide access to quality assessed gene expression datasets Rapid access to gene expression profile macrophage treated with a variety of conditions Provide datasets for Systems biology

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The GO Partition Database was designed to feature ontology partitions with GO terms of similar specificity. The GO partitions comprise varying numbers of nodes and present relevant information theoretic statistics, so researchers can choose to analyze datasets at arbitrary levels of specificity. The GO Partition Database, featuring GO partition sets for functional analysis of genes from human and ten other commonly-studied organisms with a total of 131,972 genes.

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• SciCrunch
• 17 years ago - by Anonymous

A taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts It contains single reference whole-genome sequences for each species from which we have complete mitochondrial or chloroplast data. A new release of this database also includes 42,000 new mitochondrial sequences and 39,000 new chloroplast sequences.

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• SciCrunch
• 17 years ago - by Anonymous

An annotation program which aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). It is a central dataset for other major multi-species databases, such as Ensembl and NCBI. Because of the multi-species nature of the UniProtKB, UniProtKB-GOA assists in the curation of 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. Gene Association Files can be accessed from the Downloads section of the website.

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• SciCrunch
• 16 years ago - by Anonymous

GLIDA is a database developed for those who work in the field of GPCRs-related drug discovery and need information on both GPCRs and their known ligands. It has the following characteristics: 1) A complex information system covering biological information of GPCRs as well as chemical information of their known ligands. 2) Two starting points : Enterable either by GPCR search or ligand search. 3) Cross-searchable between GPCRs and their ligands. The pages of GLIDA are continuesly updated.

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• SciCrunch
• 17 years ago - by Anonymous

Collection of male germ cell transcriptiome information derived from Serial Analysis of Gene Expression (SAGE). It includes the three key germ cell stages in spermatogenesis, including mouse type A spermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries and is by far the most comprehensive resource available. Users can choose a global view of germ cell transcriptome data in the UCSC Genome browser. They can also search genes or specify searching criteria based on tag sequence, chromosomal location or tag counts.

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• SciCrunch
• 17 years ago - by Anonymous

The Genomic Threading Database (GTD)is a fast and powerful protein fold recognition method, whichcontains structural annotations of proteomes, translated from the genomes of key organisms. GenTHREADER can be applied to either whole, translated genomic sequences (proteomes), as in the case of the GTD, or individual protein sequences, as in the case of the PSIPRED server. Annotations are made using a modified version of our recently developed GenTHREADER software.

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• SciCrunch
• 17 years ago - by Anonymous

An R package for ranking ChIP-seq peaks with shape information.

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• SciCrunch
• 13 years ago - by Anonymous