Explore NCBI(National Center for Biotechnology Information)Submitted by:Hafiz Muhammad Zeeshan RazaCIIT/FA-17/RBS-002/SWLCOMSATS INSTITUTE OF INFORMATION TECHNOLOGYSAHIWAL CAMPUSNCBI:The National Center for Biotechnology Information (NCBI) at the National Institutes of Health apart of National Library of Medicine (NLM) was created in 1988 to develop information systemsfor molecular biology. It has made sciences very advanced by providing the access to biomedicaland genomic information. It is related to large number of databases about biotechnology andbiomedicine. Major databases includes GenBank, PubMed, BLAST, Protein databases, FASTAsequences, SNPs, Genome maps, homology and many more.Basic Local Alignment Search Tool (BLAST):The most popular program was developed by Stephan Altschul of NCBI in 1990 for sequenceanalysis. BLAST uses random sequences to align a query sequence with all sequences in adatabase. The objective is to find high-scoring matching segments among related sequences. Theexistence of such segments above a given threshold indicates pairwise similarity beyond randomchance, which helps to discriminate related sequences from unrelated sequences in a database.BLAST is a family of programs which included BLASTN (for nucleotide sequence), BLASTP(for protein sequence) and BLASTX (for six reading frames). The graphical output includeshorizontal bars and a diagonal in a two-dimensional diagram showing the overall extent ofmatching between the two sequences. The BLAST web server (www.ncbi.nlm.nih.gov/BLAST/)has been designed in such a way as to simplify the task of programs election. The programs areorganized based on the type of query sequences, protein sequences, nucleotide sequences, ornucleotide sequence to be translated.Reverse PSI-BLAST (RPS-BLAST; www.ncbi.nlm.nih.gov/BLAST/) is a web-based server thatuses a query sequence to search against a pre-computed profile database generated by PSI-BLAST.CDART (Conserved Domain Architecture;www.ncbi.nlm.nih.gov/BLAST/) is a domain searchprogram that combines the results from RPS-BLAST, SMART, and Pfam. The resulting domainarchitecture of a query sequence can be graphically presented along with related sequences.PubMed (Primary MEDLINE research database):PubMed7is a free search engine accessing primarily the7MEDLINE7database7of references andabstracts on life sciences and biomedical topics. It provides collection of books, articles,references, PMC research papers, citations from journals and NCBI book shelf. We can performsimple searches by entering key aspects related to our topic. A7PMID7(PubMed identifier orPubMed unique identifier) is a unique integer value assigned to each PubMed record. PMCID isan identifier for all works published in the free to access PubMed central.The assignment of a PMID or PMCID to a publication tells the reader nothing about the type orquality of the content. PMIDs are assigned to7letters to the editor, editorial opinions, columns, andany other piece that the editor chooses to include in the journal, as well as peer-reviewed papers.The existence of the identification number is also not proof that the papers have notbeen7retracted7for fraud, incompetence, or misconduct. The announcement aboutany7corrections7to original papers may be assigned a PMID.GenBank:NCBI has the responsibility for marketing the DNA sequence databases as well as coordinateswith individual laboratories and other sequence databases such as European Molecular BiologyLaboratory (EMBL) and DNA databank of Japan (DDBJ). NCBI provides Gene, OnlineMendelian Inheritance in Man, the Molecular Modeling Database, dbSNP, the referencesequence collection, a map of the human genome and taxonomy browser also. NCBI assigns aunique identifier to each species of organism.Protein clusters:The Protein Clusters database contains >790 000 sets of almost identical RefSeq proteinsencoded by complete genomes from prokaryotes, eukaryotic organelles (mitochondria andchloroplasts), viruses and plasmids, as well as from some protozoans and plants. The clusters areorganized in a taxonomic hierarchy and are created based on reciprocal best-hit protein BLASTscores. These clusters are used as a basis for genome-wide comparison at NCBI and to providesimplified BLAST searches via Concise Microbial Protein BLAST(www.ncbi.nlm.nih.gov/genomes/prokhits.cgi). Protein Clusters provides annotations,publications, domains, structures, external links and analysis tools, including multiple sequencealignments and phylogenetic trees.Entrez:The Entrez Global query cross Database Search system is used at NCBI for all the majordatabases such as Nucleotide and Protein sequences, Protein structures, PubMed, Taxonomy,Complete Genomes, OMIM, and several others. NCBI distributed the first version of Entrez in1991, composed of nucleotide sequences from7PDB7and7GenBank, protein sequences fromSWISS-PROT, translated GenBank, PIR, PRF, PDB and associated abstracts and citations fromPubMed. Entrez is specially designed to integrate the data from several different sources,databases and formats into a uniform information model and retrieval system which canefficiently retrieve that relevant references, sequences and structures.Submission portal:To streamline the process of submitting data to NCBI databases, NCBI is creating a unifiedsubmission portal (submit.ncbi.nlm.nih.gov) that will provide a single access point to the varioussubmission interfaces. This portal should be particularly useful for submitters of complex high-throughput sequencing; genome-wide association studies (GWAS) or functional genomic datasets that involve the simultaneous submission of data to several NCBI resources. Submitters willbe able to create accounts that will track and display all of their submissions and will facilitatecommunication with relevant NCBI staff. Currently, the portal fully supports submissions to Bio-Sample, Bio-Projects and GTR, as well as to the TSA and whole genome shotgun (WGS)divisions of GenBank. It also provides links to the submission pages for 10 other