Past PubMed and BLAST: Exploring NCBI devices and databases

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Past PubMed and BLAST: Exploring NCBI devices and databases Kate Bronstad David Flynn Alumni Medical Library

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Location 12 th Floor Instructional Bldg Services Electronic assets: full content access through PubMed, Google Scholar, Web of Science Reference: drop in or by reservation Instruction: ask for class sessions or making of web instructional exercise - Learning asset focus: lab space, hands-on direction Alumni Medical Library

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National Center for Biotechnology Information Built on Entrez System Original database was Nucleotide PubMed based upon this unique structure. PubMed, GENE, other atomic databases interconnected Gene revelation, related information alternatives in PubMed MyNCBI works with different databases NCBI

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Gives succession, expression, data about protein structure and capacity. Doesn't list all known and anticipated qualities Focuses on totally sequenced genomes or ones where investigate groups are effectively contributing hereditary data. Data from RefSeq and working together model life form databases. Blend of curated and consequently redesigned data. Pulls in, connections out to assets outside of NCBI. 4.6 Million records for 5,588 taxa GENE

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Summary authority full name, quality sort, heredity, outline, AKA Genomic districts, transcripts – structure, exon-intron limits. Quality table for more full show. Book index: GeneRIF. Synopsis of quality capacities with particular references to related articles about capacity of quality/proteins in PubMed. Assembled by individuals at NCBI. Not extensive, but rather will give you the most pertinent papers with respect to work. Creators can contact the NCBI to present their references GENE Record

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Reference Sequences Nucleotide successions and protein interpretation Curated by NCBI or NCBI-endorsed programs. Contrast amongst GenBank and RefSeq GenBank has crude information and copied records Metadata in GenBank can be fragmented RefSeq commented on, curated and non-repetitive. NCBI takes best groupings from GenBank and clergymen for RefSeq records RefSeq

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mRNAs and Proteins NM_123456 Curated mRNA NP_123456 Curated Protein NR_123456 Curated non-coding RNA XM_123456 Predicted mRNA XP_123456 Predicted Protein XR_123456 Predicted non-coding RNA Gene Records NG_123456 Reference Genomic Sequence Chromosome NC_123455 Microbial replicons, organelle genomes, human chromosomes AC-123455 Alternate gatherings Assemblies NT_123456 Contig NW_123456 WGS Supercontig RefSeq Record Numbers

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Online Mendelian Inheritance in Man Previously in print, 10 volumes, overhauled at regular intervals. Contains all the known qualities in people. Gives referenced clarifications of cloning, allelic varieties, legacy, mapping, sub-atomic hereditary qualities Links to clinical and testing data OMIA (Online Mendelian Inheritance in Animals) a different database for data in creatures. OMIM

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GEO Profiles: Microarray Data Repository open store -Archives and unreservedly disseminates microarray, cutting edge sequencing, and other high- throughput practical genomic information. - Submitted by specialists. Offers information storage, electronic interfaces and applications to question and download content Evidence Viewer: Graphical show of proof supporting a quality model Databases for Evidence

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Genome Sequence and guide information from the entire genomes of more than 1000 creatures - Represent life forms that are totally sequenced and those that are in advance. Graphical outlines of finish genomes/chromosomes Specialized genome BLAST pursuit to see arrangements in setting of genome Good for microbial genomes.

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May need to use rather than BLAST if searching for a model creature with same capacity or if taking a gander at a transformative examination. Permits downloads of genomic data. - Can catch administrative district by including bases up or down stream. Various and pairwise arrangement Protein Alignment scores -Substitution rates, synonymous versus non, conservative versus radical Polymorphisms in GeneView dbSNP connect Homologene

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Structure, MMDB (Molecular Modeling Database) -Access from Protein interface, Related Structure CN3D for application to see at various points, highlight succession in structure. Immense (Vector Alignment Search Tool) looks by geometric criteria Structure and Models

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BLAST Link Pre-run BLAST comes about NCBI runs week after week scans for each new protein arrangement. Can use as opposed to running BLAST look -More data than in default BLAST: taxonomy report, see numerous alignments, search information against various BLink

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MGI Ensembl KEGG: Kyoto reference book of qualities and genomes - Integrated databases - Pathway, malady, tranquilize - Good for fast pathway and protein representation UCSC Genome Browser - Visualize tracks to think about data like quality expectations, ESTs, moderated districts. - BLAT Blast-like arrangement device – faster yet not as touchy as BLAST. Connections to Outside Databases

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Gene expression data from Gene Ontology (GO) - Lists what has been allocated to the quality in: Molecular Function Biological Processes Cellular Component Level of proof and references connected when accessible. Joins into AMIGO program for more metaphysics or confirmation data Can hunt GENE down GO data by putting postfix at end of pursuit Ex: "vasodilation [GO]" Gene Information from GO

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Biostatistics - Dr.Mayetri Gupta: made factual programming for finding translation calculate restricting destinations (themes) and administrative modules, quality administrative systems, and phylogenetic surmising. Dr. Paola Sebastiani: made programming for system demonstrating called Bayesware Discoverer, likewise CAGED, BAGED for investigation of quality expression information. BU Resources

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Contact the library with any proposals, suggestions that we can list or advance for BU people group Software and datasets can be documented in BU's Digital Common If there are assets we don't have, we might have the capacity to acquire them for you. Hands-on BLAST workshop advertised. Library Support