In this article we will discuss about the gene structure predications in plant genomics.
Since the outcome of USA National Genomic Initiative (NGPI) in 1998, initiation for plant genetic, molecular and applied research has dramatically changed. In the gene structure prediction for plant genomes one of the server gene seqer @ plant GDB help to address to plant genome annotation.
This server integrates up-to-date public plant genome records. Plant GDB allowing the robust annotation of plant genomic sequences using both native and homologous EST cDNA and protein sequences.
Initial gene predictions were designed to locate proteins coding exons with the short fragments genomic DNA. However, advancement in sequencing technology promoted the development of novel (algorithms) capable of predicting and assembling exons into multiple gene structure on both strand of single genomic fragment.
The gene seqer @ Plant GDB server relies on many steps. Initially, the user selects on appropriate model for splice site prediction and supplies to genomic DNA sequence. The sequence can be uploaded from a local disc pasted by a Gen Bank accession number. The user may choose to have collection of ESTS on full length cDNA.
After submission, the server returns interactively to the browser results in splice alignment. The web output of the Gene sequencer (a) plant GDB server including graphic summary of the predicted gene structure encoded proteins. The protein sequences are linked to the NCBI Blast Server. Which in turn may be used as probe for further spliced alignment?
EN Trez:
The EN Trez system often provides access to nucleotide and protein sequence databases. It is basically a molecular biology database retrieval system, developed by National Centre for Biotechnology Information (NCBI). A molecular modeling 3D structure database (MMDB), a genome maps database is accessed by the Entrez system.
The literature database, PubMed, provides excellent and easy access to MEDLINE and price ME DLINE articles. The taxonomy database contains more than 25,000 different species. The retrieval of DNA and proteins for any taxonomic groups are entitled by this taxonomy database.
SRS:
SRS is a homologous interface to over 80 biological databases that have been developed at the European Bioinformatics Institute (EBI) at Hinxton, UK. Various nature of databases are available such as sequences related to metabolic pathways, transcription factors, application results (example, BLAST), protein 3-D structure, genome mapping and mutations.
DBGET:
It is an integrated database retrieval system developed by the Institute for Chemical Research Kyoto University and University of Tokyo, available through genome NET. The DBGET provides access to about 20 databases which are queried one at a time.
One of the advantages of specific features of DBGET is search directly with a specific entry and provides list of links to all of the database entries. It also connects directly with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. DBGET has limited search methods than either SKS or Entrez.