Bamboo-infoline: A database for North Bengal Bamboo's

Bamboo, the "Green Gold", included in the non-timber forest products has both ecological and economic importance. Here is an attempt to describe a database named "Bambooinfoline" , which provides enumeration of the different species of bamboos found in North Bengal, with special emphasis on taxonomy, edible properties, chemical constituents, morphological features along with tissue culture specifications, which in turn benefits of scientific community. AVAILABILITY: The database is freely available at http://www.bamboodb.ind.in/     

Ssa miRNAs DB: Online repository of in silico predicted miRNAs in Salmo salar

The Atlantic salmon (Salmo salar) is a very valuable commercial salmonid species. As with other aquaculture species, intensive aquaculture of Atlantic salmon often faces disease problems especially in early life stages which can limit stable production of the species. 'Ssa miRNAs DB', a bioinformatics and manually curated database, aims at providing a comprehensive resource of microRNA in Altantic salmon, with a user friendly interface for a convenient retrieval of each entry by microRNA ID or target gene. The current version of Ssa miRNAs DB involved the prediction of 41 and 266 homologous and novel microRNAs, respectively. AVAILABILITY: The database is available for free at http://www.molgenv.com/ssa_mirnas_db_home.php.     

Phyto-mellitus: A phyto-chemical database for diabetes

Herbs are the base used for treatment in Ayurveda. We describe a database named Phyto-Mellitus with information on plants traditionally used for diabetes with their chemical constituents. The active principles of these plants are antioxidant and free radical scavenging.

Availability

http://www.bicmlacw.org/bt/     

Peripartum cardiomyopathy: the need for a national database

Peripartum cardiomyopathy (PPCM) is a rare and life-threatening disease that affects young women in the last month of pregnancy or within 5 months of delivery. It is a form of dilated cardiomyopathy with left-sided systolic dysfunction. The incidence rate in the Western world is estimated to be 1:3000. Symptoms of PPCM vary greatly and may be obscured by common physiological aspects of pregnancy. Therefore, the incidence rate might be higher. Echocardiography or MRI can confirm or rule out PPCM. Unfortunately, there is no specific risk factor profile available. The clinical course varies from complete recovery to deterioration of cardiac function. Patients with PPCM, especially those whose ventricular function has not returned to normal, are advised against further pregnancy. Recently, more disease-specific therapeutic strategies have been developed with promising results for prolactin blockade by bromocriptine. Increasing awareness for PPCM among general practitioners, gynaecologists and cardiologists may help to diagnose patients efficiently in order to start adequate treatment. A national registry is warranted to identify risk factor profiles and to optimise treatment strategies.     

HORA suite: a database and software for human metabolomics

HORA suite (Human blOod Range vAlidator) consists of a Java application used to validate the metabolomic analysis of human blood against a database that stores the normal plasma and serum range concentrations of metabolites. The goal of HORA is to find the metabolites that are outside the normal range and to show those not present in the list provided by the user, for different thresholds of concentration. Moreover it supplies a graphical interface to manage the data. The software can also be used to compare different metabolomic techniques. HORA is open-source software and it can be accessed at . A separate file contains instructions for the installation and a brief tutorial.     

Competition between mobile species using patchy resources: an example from a freshwater,symbiotic assemblage

Summary Three species of freshwater mites that are symbiotic with mussels in St Mark's River, north Florida, have consistently high rates of colonization to and occupy high proportions of mussels. The mites Unionicola poundsi and U. serrata are territorial and have limited numbers/host, whereas the non-territorial U. abnormipes has highly variable numbers/host. U. abnormipes and U. serrata are most common in Villosa villosa and Uniomerus declivis respectively, patterns that can not be explained by host species preferences, whereas U. poundsi is equally abundant in both host species. Field experiments showed that both U. poundsi and U. serrata were limited most by intraspecific competition between adult mites, presumably for access to food and oviposition sites. Additionally, U. serrata did not remain within small hosts, most of which were V. villosa. In contrast, numbers of U. abnormipes were limited by both other mite species although the nature of the interactions differed. U. serrata may prey on U. abnormipes when they co-occur, whereas U. poundsi probably only excludes U. abnormipes from certain areas within hosts. Hence, U. abnormipes occurs mostly in V. villosa because most of these mussels do not contain U. serrata, but even so its numbers are still depressed by U. poundsi. The results were consistent with the general expectation of Holmes and Price (1986) that parasite assemblages where species have high colonization levels should be organized primarily by biotic interactions. However, specific outcomes of competition between mites were consistent with the more general model of Levins (1979) for competition between species using variable resources. Failure of other models to apply to Unionicola pinpointed at least five key biological characters that may form a better basis of comparison than taxonomic or habitat-based contrasts.     

PeroxiBase: a class III plant peroxidase database

Class III plant peroxidases (EC 1.11.1.7), which are encoded by multigenic families in land plants, are involved in several important physiological and developmental processes. Their varied functions are not yet clearly determined, but their characterization will certainly lead to a better understanding of plant growth, differentiation and interaction with the environment, and hence to many exciting applications. Since there is currently no central database for plant peroxidase sequences and many plant sequences are not deposited in the EMBL/GenBank/DDBJ repository or the UniProt KnowledgeBase, this prevents researchers from easily accessing all peroxidase sequences. Furthermore, gene expression data are poorly covered and annotations are inconsistent. In this rapidly moving field, there is a need for continual updating and correction of the peroxidase superfamily in plants. Moreover, consolidating information about peroxidases will allow for comparison of peroxidases between species and thus significantly help making correlations of function, structure or phylogeny. We report a new database (PeroxiBase) accessible through a web server with specific tools dedicated to facilitate query, classification and submission of peroxidase sequences. Recent developments in the field of plant peroxidase are also mentioned.     

MPDB 1.0: a medicinal plant database of Bangladesh

The term of medicinal plants include a various types of plants used in herbalism with medicinal activities. These plants are considered as rich resources of ingredients which can be used as complementary and alternative medicines and, also in drug developments and synthesis. In addition, some plants regarded as valuable origin of nutrition. Thus, all these plants are recommended as therapeutic agents. Information related to medicinal plants and herbal drugs accumulated over the ages are scattered and unstructured which make it prudent to develop a curated database for medicinal plants. MPDB 1.0 database is dedicated to provide the first window to find the plants around Bangladesh claimed to have medicinal and/or nutritive values by accumulating data from the published literatures. This database contains 406 medicinal plants with their corresponding scientific, family and local names as well as utilized parts for treatment from different districts of Bangladesh. Information regarding ailments is available for 353 plants. In addition, we have found active compounds for 78 plants with their corresponding PubMed ID.

Availability

www.medicinalplantbd.net     

CancerLectinDB: a database of lectins relevant to cancer

The role of lectins in mediating cancer metastasis, apoptosis as well as various other signaling events has been well established in the past few years. Data on various aspects of the role of lectins in cancer is being accumulated at a rapid pace. The data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. Not only do the lectins vary significantly in their individual functional roles, but they are also diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their potential applications. An organization of these seemingly independent data into a common framework is essential in order to achieve effective use of all the data towards understanding the roles of different lectins in different aspects of cancer and any resulting applications. An integrated knowledge base (CancerLectinDB) together with appropriate analytical tools has therefore been developed for lectins relevant for any aspect of cancer, by collating and integrating diverse data. This database is unique in terms of providing sequence, structural, and functional annotations for lectins from all known sources in cancer and is expected to be a useful addition to the number of glycan related resources now available to the community. The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for individual lectins pertain to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value for various studies on lectin cancer biology. CancerLectinDB can be accessed through . Availability: CancerLectinDB is available freely for academic use from , Contact nchandra@serc.iisc.ernet.in for further information.     

NemChR-DB: a database of parasitic nematode chemosensory G-protein coupled receptors

Nematode Chemosensory G-Protein Coupled Receptors have expanded within nematodes, where they play important roles in foraging and host-seeking behaviour. Nematode Chemosensory G-Protein Coupled Receptors are most highly expressed during free-living stages when chemosensory signalling is required for host detection and nematode activation in various parasitic nematodes, and therefore position Nematode Chemosensory G-Protein Coupled Receptors at the transition from infective to parasitic stages, making them important regulators to study in terms of host-seeking and host specificity. To facilitate the analysis of Nematode Chemosensory G-Protein Coupled Receptors, here we describe an integrative database of nematode chemoreceptors called NemChR-DB. This database enables users to study diverse parasitic nematode chemoreceptors, functionally explore sequence entries through structural and literature-based annotations, and perform cross-species comparisons.     

Gene centres,a source for genetic variants in symbiotic nitrogen fixation: Host-induced ineffectivity inPisum sativum ecotype fulvum

Summary Pisum sativum ecotype fulvum forms ineffective nodules with Rhizobium strains, isolated from effective nodules of the cultivated pea in Europe. Rhizobium strains isolated from nodules of fulvum peas in Israel are fully effective on this host plant, but in association with the cultivated pea they induce nodules of poor N₂-fixing activity. The distribution of these fulvum-specific Rhizobium strains is restricted to regions where the fulvum pea occurs naturally. Rhizobium strains from other geographical regions induce mainly ineffective, or partially effective nodules on fulvum plants.A wide genetic variation, with regard to symbiotic response to a standard set of Rhizobium strains, was demonstrated in the fulvum plants collected in Israel. Based on variation in N₂-fixation three groups of plants can be distinguished. These plants offer the possibility for the study of host-genetic control on symbiotic nitrogen fixation.     

MEDDB: a medicinal plant database developed with the information gathered from tribal people in and around Madurai, Tamil Nadu

Tribal peoples are endowed with enriched traditional wisdom to use available nature resources around them. They are well versed in the usage of plant for treating various diseases. They have used powder or extract or paste form of the plant parts such as root, shoot, whole plant, fruits and leaves etc. The recipe known by the tribal people was passed on only to their family members and community through mouth to mouth practice. Hence, the knowledge is confined to particular people alone. It is always expedient to store information in the database, so that it will be accessible by everyone from everywhere. To achieve this, MEDDB has been developed, which stores the details of 110 plant species that are commonly used by tribes for fever, asthma, cold, cough, diabetes, diarrhea, dysentery, eye infections, stomach ache, wounds and snake bite. The details of each plant were collected from the literature and through web search to give comprehensive and exhaustive information. Each plant entry is compiled under the subheadings viz., common name, classification, physical characteristics, medicinal uses, active constituents, and references.     

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi

Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URL http://unite.zbi.ee     

Gene expression normalization in a dual-compartment system: a real-time quantitative polymerase chain reaction protocol for symbiotic anthozoans

Traditional real-time quantitative polymerase chain reaction protocols cannot be used accurately with symbiotic organisms unless the relative contribution of each symbiotic compartment to the total nucleic acid pool is known. A modified 'universal reference gene' protocol was created for reef-building corals and sea anemones, anthozoans that harbour endosymbiotic dinoflagellates belonging to the genus Symbiodinium. Gene expression values are first normalized to an RNA spike and then to a symbiont molecular proxy that represents the number of Symbiodinium cells extracted and present in the RNA. The latter is quantified using the number of genome copies of heat shock protein-70 (HSP70) amplified in the real-time quantitative polymerase chain reaction. Gene expression values are then normalized to the total concentration of RNA to account for differences in the amount of live tissue extracted among experimental treatments and replicates. The molecular quantification of symbiont cells and effect of increasing symbiont contributions to the nucleic acid pool on gene expression were tested in vivo using differentially infected sea anemones Aiptasia pulchella. This protocol has broad application to researchers who seek to measure gene expression in mixed organism assemblages.     

dbVOR: a database system for importing pedigree,phenotype and genotype data and exporting selected subsets

Background

When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the overlap can introduce several kinds of problems. Most times the overlapping genotypes are the same, but sometimes they are different. Occasionally, the lab will return genotypes using a different allele labeling scheme (for example 1/2 vs A/C). Sometimes, the genotype for a person/marker index is unreliable or missing. Further, over time some markers are merged and bad samples are re-run under a different sample name. We need a consistent picture of the subset of data we have chosen to work with even though there might possibly be conflicting measurements from multiple data sources.

Results

We have developed the dbVOR database, which is designed to hold data efficiently for both genome-wide and targeted experiments. The data are indexed for fast retrieval by person and marker. In addition, we store pedigree and phenotype data for our subjects. The dbVOR database allows us to select subsets of the data by several different criteria and to merge their results into a coherent and consistent whole. Data may be filtered by: family, person, trait value, markers, chromosomes, and chromosome ranges. The results can be presented in columnar, Mega2, or PLINK format.

Conclusions

dbVOR serves our needs well. It is freely available from https://watson.hgen.pitt.edu/register. Documentation for dbVOR can be found at https://watson.hgen.pitt.edu/register/docs/dbvor.html.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0505-4) contains supplementary material, which is available to authorized users.     

Transgenic Plant Monitor (TPM): a relational database for the management and analysis of information in plant tissue culture and transformation laboratories

Increased public concern and strict statutory regulations relating tothe generation and exploitation of genetically modified organisms, make itimperative to track accurately individual plants through DNA transformationprogrammes. The ability to rapidly retrieve information associated withspecifictransgenic events and to provide accurate reports on demand is an increasinglyimportant feature for public research laboratories. Transgenic Plant Monitor(TPM) has been developed as a database structured to allow efficient recording,monitoring and analysis of the extensive and complex data generated in planttissue culture and transformation experiments. TPM is built upon the widelyavailable Microsoft Access database engine and can be readily adoptedand/or adapted by other users. The key features and the utility of TPM as aresearch tool are discussed in this article.     

DigiPINS: a database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies

Single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variations in numerous organisms, have emerged as important tools for the study of complex genetic traits and deciphering of genome evolution. High-throughput genome sequencing projects worldwide provide an unprecedented opportunity for whole-genome SNP analysis in a variety of species. To facilitate SNP discovery in vertebrates, we have developed a web-based, user-friendly, and fully automated application, DigiPINS, for genome-wide identification of exonic SNPs from EST data. Currently, the database can be used to the mining of exonic SNPs in six complete genomes (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus and Danio rerio). In addition to providing information on sequence conservation, DigiPINS allows compilation of comprehensive sets of polymorphisms within cancer candidate genes or identification of novel cancer markers, making it potentially useful for cancer association studies. The DigiPINS server is available via the internet at http://pbil.univ-lyon1.fr/gem/DigiPINS/query_DigiPINS.php.