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BLAST FTP Site CDD Structure (MMDB)COG Trace ArchiveGENSAT UniGeneGenBank UniVecWhole Genome Shotgun Sequences GenPept Gene dbGAP OpenAccess DataGene Expression Nervous System Atlas (GENSAT) dbMHC DataGene Expression Omnibus (GEO) Profiles and Datasets RSS FeedsGenome SequinGenome Markers (UniSTS) tbl2asnHomoloGene Batch EntrezMapping Data CDTreeNCBI Taxonomy Cn3DProtein Clusters EUtilitiesPubChem NCBI ToolboxRefSeq ProSplignSKY/MFish and CGH Data Splign Sequence Read Archive
● Use of boolean terms for search– AND– OR– NOT
● General syntax:– term [field] OPERATOR term [field]
● Use of brackets to combine the terms
Accession ACCN YES YES YES YES YESAll Fields ALL YES YES YES YES YESAuthor Name AUTH YES YES YES YES YESEC/RN Number ECNO YES YES YES YES YESFeature Key FKEY YES NO YES NO YESFilter FILT YES YES YES YES YESGene Name GENE YES YES YES NO YESIssue ISS YES YES YES YES YESJournal Name JOUR YES YES YES YES YESKeyword KYWD YES YES YES NO YESModification Date MDAT YES YES YES YES YESMolecular Weight MOLWT NO YES NO NO NOOrganism ORGN YES YES YES YES YESPage Number PAGE YES YES YES YES YESPrimary Accession PACC YES YES YES NO YESProperties PROP YES YES YES NO YESProtein Name PROT YES YES YES NO YESPublication Date PDAT YES YES YES YES YESSeqID String SQID YES YES YES NO YESSequence Length SLEN YES YES YES NO NOSubstance Name SUBS YES YES NO YES NOText Word WORD YES YES YES YES YESTitle Word TITL YES YES YES NO NOVolume VOL YES YES YES YES YES
Field Short term Nucleotide Protein Genome Structure PopSet
Available for Database
Affiliation AD All Fields ALLAuthor AU Corporate Author CNEC/RN Number RN Entrez Date EDATFilter FILTER First author IAUFull Author Name FAU Grant Name GRIssue IP Investigator IRJournal Title TA Language LAMeSH Date MHDA MeSH Major Topic MAJRMeSH Subheadings SH MeSH Terms MHNLM Unique ID JID Other Term OTPagination PG Personal Name as Subject PSPharmacological Action PA Place of Publication PLPublication Date DP Publication Type PTPublisher Identifier AID Secondary Source ID SISubset SB Substance Name NMText Word TW Title TITitle / Abstract TIAB Unique Identifiers UIDVolume VI
Field Short term Field Short term
PubMed ENTREZ search fields
● Range operator “:” (ACCN, MOLWT, SLEN)– x : y [SLEN]– works with dates; molecular weight
● For more information: http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
Summary Default display, hotlinked Accession number and brief description
Nucleotide, Protein, CoreNucleotide, EST, GSS, PopSet, Genome, Genome Project
Brief
Hotlinked Accession number and abbreviated description, hotlinked project number in the case of a genome project
Nucleotide, Protein, CoreNucleotide, EST, GSS, PopSet, Genome, Genome Project
GenBank Full report formatNucleotide, Protein, CoreNucleotide, EST, GSS, Genome
GenPept Full report format Protein
GenBank (full)
Complete GenBank record with all features and all Sequence. This format is useful for very large GenBank records
Nucleotide, Protein, CoreNucleotide, EST, GSS, Genome
GenPept
Complete GenPept record with all protein features and all Sequence. This format is useful for very large GenBank records
Protein
DisplayFormat
Description Databases Available
INSDSeq XML XML DTD for sequence records Nucleotide, Protein
GI list List of GenInfo – GI indentifiers Nucleotide, Protein, CoreNucleotide, EST, GSS,
ASN.1
Abstract syntax Notation One, used data storage and retrieval and to help achieve interoperability among platforms
Nucleotide, Protein, CoreNucleotide, EST, GSS, PopSet, Genome
EST Native display format for Expressed Sequence Tag records
EST
Graphics orGraph
The graphical view of the sequence accessible by selecting the hotlinked Accession numbers
Nucleotide, Protein and Genome
TinySeq XML Simplified XML for parsingNucleotide, Protein, CoreNucleotide, EST, GSS, Genome
DisplayFormat
Description Databases Available
GSSNative Display format for the Genome Survey Sequences GSS
Overview
Tabular-layout of data including Links to BLAST results, CDD, ftp site and general information for a genome in Genomes; for Genome Project database it is a complete display of links to projects in the database, serves as a portal to links to all projects in the database about the organism specific genome
Genome, Genome Project
PopSet summary
The number set of Accession Numbers comprising the PopSet accessible by selecting the hotlinked PopSet Acession Numbers
PopSet
XML Script-parseable formatNucleotide, Protein, Genome
DisplayFormat
Description Databases Available
UI List List of database ID's PopSet