bioinformatics-da...
Follow
Find
3.5K views | +3 today
 
bioinformatics-databases
Bioinformatics - Databases
Your new post is loading...
Your new post is loading...
Scooped by Dr. Stefan Gruenwald
Scoop.it!

DroSpeGe: Drosophila Species Genomes

DroSpeGe: Drosophila Species Genomes | bioinformatics-databases | Scoop.it

Aphid Genome
Transcriptome expression
Daphnia genome
Gene gain/loss in GO groups

About DroSpeGe paper
New D. melanogaster Genes & Exons
BioMart : DroSpeGe
TeraGrid "flies" fast for genomes
Common Chromosomes
Twelve Genomes !

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

Inparanoid - Ortholog Groups with Inparalogs

Inparanoid - Ortholog Groups with Inparalogs | bioinformatics-databases | Scoop.it
more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

RNA Bricks - a database of RNA 3D structure motifs and their interactions

RNA Bricks - a database of RNA 3D structure motifs and their interactions | bioinformatics-databases | Scoop.it
Database of recurrent RNA 3D structure motifs and their interactions (hydrogen bonds and close contacts), found in experimentally determined RNA structures and in RNA-protein complexes.


Currently you can find here over 2600 RNA structures and RNA-protein complexes from the PDB (see statistics for details). We hope that your favorite ones are in. If not, keep visiting us - the database is updated weekly.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

IGDB.NSCLC: Integrated Genomic Database of Non-Small Cell Lung Carcinoma

IGDB.NSCLC: Integrated Genomic Database of Non-Small Cell Lung Carcinoma | bioinformatics-databases | Scoop.it

CANCER is the leading cause of human mortality resulted in 7.9 million deaths in 2007 and projected to be over 11 million deaths in 2030 worldwide. LUNG CANCER is the most common cause of cancer-related mortality over the last 30 years accounted for 1.4 million deaths in 2008. Despite recent advances in diagnosis and treatment, the prognosis of lung cancer patients remains dismal with an overall 5-year survival of <15%. Discovery of novel targets and therapeutic strategies is urgently needed.


IGDB.NSCLC database is aiming to facilitate and prioritize identified lung cancer genes and microRNAs for pathological and mechanistic studies of lung tumorigenesis and for developing new strategies for clinical interventions. We integrated and curated various lung cancer genomic datasets to present


1. lung cancer genes with somatic mutations, experimental supports and statistic significance in association with clinicopathological features;

2. genomic alterations with copy number alterations (CNA) detected by high density SNP arrays, gain or loss regions detected by arrayed comparative genome hybridization (aCGH), and loss of heterozygosity (LOH) detected by microsatellite markers;

3. aberrant expression of genes and microRNAs detected by various microarrays.


IGDB.NSCLC database provides user friendly interfaces and searching functions to display multiple layers of evidence for detecting lung cancer target genes and microRNAs, especially emphasizing on concordant alterations:


1. genes with altered expression located in the CNA regions;

2. microRNAs with altered expression located in the CNA regions;

3. somatic mutation genes located in the CNA regions; and

4. genes associated with clinicopathological features located in the CNA regions.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

PBmice - PiggyBac Mutagenesis Information Center

PBmice - PiggyBac Mutagenesis Information Center | bioinformatics-databases | Scoop.it

PBmice is based on the April 2007 Mus musculus (strain C57BL/6J) high coverage assembly (NCBIm37,GCA_000001635.18

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

PDZBase - A protein-protein interaction database

PDZBase - A protein-protein interaction database | bioinformatics-databases | Scoop.it

PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. PDZBase currently contains 339 experimentally determined protein protein interactions. For more information, visit the PDZBase help pages or contact us at pdzbase@med.cornell.edu.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

Hymenoptera Genome Database

Hymenoptera Genome Database | bioinformatics-databases | Scoop.it

With over 115,000 described species, the order Hymenoptera comprises approximately 10% of the species diversity on Earth. The largest described family in the order, Icheumonidae, contains more species than all species of birds and mammals combined! This group of 'membrane-winged' insects includes sawflies, bees, ants and wasps, which directly affect human health and agriculture through diverse roles such as pollinators, pests and parasitoids.


The Hymenoptera Genome Database (HGD) is an informatics resource supporting genomics of insect species of this order. HGD provides access to the genomes of bees Apis melliferaBombus terrestris and B. impatiens, the parasitoid wasp Nasonia vitripennis, and seven species of ants available through the Ant Genomes Portal. It will soon incorporate genome databases for two additional species of bees, Apis dorsata and A. florea, as well as two additional species of ants. Combining these species into a single resource allows biologists to leverage the genome information, and enhances the value of genomic data for each species by facilitating cross-species comparisons.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

BloodExpress - A Web Server to Browse Gene Expression in Mouse Haematopoiesis

BloodExpress - A Web Server to Browse Gene Expression in Mouse Haematopoiesis | bioinformatics-databases | Scoop.it

Haematopoiesis (blood formation) has long served as a model process for studying stem cells and represents the best characterised adult stem cell system with functional assays and purification strategies for a plethora of precursors ranging from the pluripotent haematopoietic stem cell (HSC) via multipotent and unipotent progenitors to at least 14 distinct mature cell types.  Transcriptional control is a key factor controlling haematopoiesis. 

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

HOWDY - Human Organized Whole genome Database Top Page

HOWDY - Human Organized Whole genome Database Top Page | bioinformatics-databases | Scoop.it

HOWDY (Human Organized Whole genome Database) is a database system for retrieve human genome information in different data sources that are available to public. Sources of HOWDY are 14 public databases. The information you could find here is automatically extracted from the genetic databases and shown with all data having the identifiers in common and linking to one another. HOWDY facilitates obtaining information of human genes by using official symbols and aliases. HOWDY is daily updated.


HOWDY: an integrated database system for human genome research. Hirakawa M. Nucleic Acids Research, 30:152-157, 2002

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

GENES.MIT.EDU

GENES.MIT.EDU | bioinformatics-databases | Scoop.it

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

MyHits - An interactive resource for protein annotation and domain identification

MyHits - An interactive resource for protein annotation and domain identification | bioinformatics-databases | Scoop.it

Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

Het-PDB Navi. v1.5.5: Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms

Het-PDB Navi. v1.5.5: Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms | bioinformatics-databases | Scoop.it

Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms.


PDB is a database for protein three-dimensional structures, but the data in PDB are often obtained with bound non-standard components such as DNA, RNA, ATP, GTP, PLP and so forth. As number of proteins in PDB increases, we realized that a wealth of information for small molecule-protein interactions is buried in PDB.


The interactions found in PDB can be treated as a general template for interaction between a protein and a small molecule, such as ATP, GTP and drugs.


We have, hereby, launched Het-PDB Navi. as a starter for classification and data retrieval system of protein-small molecule interactions from PDB.


The database is focused on small molecules and does not treat macromolecules such as DNA and RNA. The database was initially developed at Nagoya University in 1999, and transferred to Nagahama Institute of Bio-Science and Technology in 2003.


The database has been maintained by Prof. Mitiko Go's laboratory from the beginning.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

SuperTarget - an extensive web resource for analyzing 332828 drug-target interactions

SuperTarget - an extensive web resource for analyzing 332828 drug-target interactions | bioinformatics-databases | Scoop.it
SuperTarget 2; AG Preissner; Charite Berlin
more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

BSDB - Bio-molecule Stretching Database

BSDB - Bio-molecule Stretching Database | bioinformatics-databases | Scoop.it

The Biomolecule Stretching Database (BSDB) contains information related to mechanical stretching of biomolecules. Currently, the database is restricted to proteins and to stretching at constant velocity.When plotting the force of resistance to pulling, F, versus the pulling distance, d, one may encounter one or more isolated force peaks on the way to full stretching. the characteristic scale of F is characterized byFmax - the maximum force in an isolated force peak. If no force peak develops, Fmax is assigned a value of zero. Usually, this happens when some disulphide bonds prevent full stretching.


The Database lists results obtained theoretically within a structure-based coarsegrained model, initially, for 17 134 structures with no more than 250 amino acids as discussed in reference: M. Sikora, J. I. Sułkowska, and M. Cieplak, Mechanical strength of 17 134 model proteins and cysteine slipknots, PLoS Computational Biology, 5 e1000547 (2009). The database is further described in: M. Sikora, J. I. Sulkowska, B. S. Witkowski, and M. Cieplak, BSDB: the biomolecule stretching database, Nucl. Acid Res. 39, D443-D450 (2011).


Multi-domain proteins are discussed in reference: M. Sikora and M. Cieplak. Mechanical stability of multi-domain proteins and novel mechanical clamps, Proteins: Struct. Funct., and Bioinf. 79(6) 2011, where 315 proteins are considered.


In the first two papers, we have used terms "cysteine knot" and "cysteine slipknots" instead of the correct terms "cystine knot" and "cystine slipknot" respectively. Further analysis of the cystine slipknot proteins can be found in reference: L. Peplowski, M. Sikora, W. Nowak, and M. Cieplak, Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations, J. Chem. Phys. 134, 085102 (2011).


It also lists experimental results on Fmax that are available in the literature. Furthermore, it provides information on Fmax as obtained within all-atom simulations. The users are encouraged to submit new theoretical and experimental entries to us and to request calculations for proteins that are not yet stored in BSDB.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

Integrated Microbial Genomes (IMG) Data Management & Analysis Systems

Integrated Microbial Genomes (IMG) Data Management & Analysis Systems | bioinformatics-databases | Scoop.it

 The mission of the Integrated Microbial Genomes (IMG) system is to support the annotation, analysis and distribution of microbial genome and metagenome datasets sequenced at DOE's Joint Genome Institute (JGI). IMG is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and metagenome datasets, as long as they agree with the IMG data release policy and follow the metadata requirements for integrating data into IMG (IMG submission site).

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

IGRhCellID: Integrated Genomic Resources of human Cell Lines for Identification

IGRhCellID: Integrated Genomic Resources of human Cell Lines for Identification | bioinformatics-databases | Scoop.it

IGRhCellID database integrates 7 common authentic tools from public domains and profiles of genomic alterations from our laboratory of common human cell lines to reduce or eradicate long standing concerns of cell misidentification. Moreover, profiles of genomic alterations of common human cell lines further allow users to select cell lines with designated genetic background. For examples, users can select a cell line with homozygous deletion of a gene to serve as indigenous knock-out human cell modelwith amplification of a gene to serve as cell model for therapeutic drug testing, and with common alterations in multiple human cell lines for common altered cancer genes across cancer types


more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

Protein Structural Change DataBase

Protein Structural Change DataBase | bioinformatics-databases | Scoop.it

The purpose of this database is to represent the relationship between protein structural change and ligand binding. We classified protein structural changes into 7 classes blow, in terms of the ligand binding sites and the location where the dominant motion occurs.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

Inter-Chain Beta-Sheet (ICBS) Database

Inter-Chain Beta-Sheet (ICBS) Database | bioinformatics-databases | Scoop.it

A database of protein-protein interactions mediated by interchain ß-sheet formation



more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

TrSDB - A Proteome Database of Transcription Factors

TrSDB - A Proteome Database of Transcription Factors | bioinformatics-databases | Scoop.it

TrSDB is a Biological Proteome KnowledgeBase linking IPI and SPTR-NR based Proteome analyses with TranScoutTransMem and ProtLoc and offering crosslinks with other relevant information from worldwide highly acknowledged biodatabases such as SWISS-PROTNCBI RefseqEnsemblInterPro or Gene Ontology Annotation

Curated complex Analyses of IPI proteomes can also be looked up, with emphasis in predicted hot entries. 

Full data of TranScoutTransMem and ProtLoc Proteomes processing can be freely downloaded

Take a look at Bibliography and Resources

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

HuRef: Diploid Human Genome Browser

HuRef: Diploid Human Genome Browser | bioinformatics-databases | Scoop.it

This browser enables access to the diploid genome sequence of J. Craig Venter as recently published in PLoS Biology. The graphical interface depicts the haploid sequence with SNP and insertion/deletion DNA variants as identified by genome assembly and comparison methods. The interface also represents the haplotype blocks from which diploid genome sequence can be inferred and gene annotations. This work was done at the J. Craig Venter Institute, with collaborators from The Hospital for Sick Children in Toronto, Canada, University of California, San Diego, and Universidad de Barcelona, Spain.

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

The 1000 Genomes Selection Browser 1.0: A database of signatures of natural selection in the human genome

The 1000 Genomes Selection Browser 1.0: A database of signatures of natural selection in the human genome | bioinformatics-databases | Scoop.it
A database of signatures of natural selection in the human genome
more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

Protein-Protein Interfaces Database

Protein-Protein Interfaces Database | bioinformatics-databases | Scoop.it

The two-chain protein interface in our definition was composed of interacting residues and nearby residues, respectively. The interfaced residues was picked up first. If the distance of any two atoms between residues is less than their sum of van der Waals radii plus 0.5 Angstrom, both residues were registered as the interfaced residues. When assigned interface residues was less than 10 residues, an arbitrary but reasonable number to reflect the minimum requirement of contact, the interface was considered as a result of crystal packing force. Therefore, it would not be considered further. To enable illuminating the types of architectures at the interface, residues whose alpha carbon atom is within a distance of 6.0 Angstrom from an alpha carbon atom of previous assigned interface residues, are included and named nearby residue. The 6.0 Angstrom selected from trial and error is very close to the lowest distance to include residues not involving in interface but essential for demonstrating the scaffold of the interface.


In this study, we have surveyed exhaustively the structures of protein-protein interfaces in PDB to carry out the structural comparisons of the interfaces. This works is an extension of the Nussinov and coworkers study (Tsai et al, 1996)

more...
No comment yet.
Scooped by Dr. Stefan Gruenwald
Scoop.it!

HitPredict - High confidence protein-protein interactions database

HitPredict - High confidence protein-protein interactions database | bioinformatics-databases | Scoop.it

HitPredict is a resource of high confidence protein-protein interactions. Interactions can be searched and downloaded with their predicted confidence level.


Protein-protein interactions from IntAct, BIOGRID and HPRD are combined, annotated and assigned a reliability score in order to identify a high confidence subset.


The reliability score is calculated as the Likelihood Ratio using naive Bayesian networks combining sequence, structure and functional annotations of the interacting proteins.


HitPredict has 239584 protein-protein interactions across 9 species, 168458 of which are predicted to be of high confidence.


more...
No comment yet.