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Links to STS records are not supplied directly from the LocusLink browse lists. The Map section of the report page, however, may include names of STS markers that are calculated, by electronic PCR, to detect cDNAs representing the gene. If there is a mv link displayed for the gene or any STS, use the Map Viewer to find additional STS in the region. Also, if a UniGene link is displayed ( on the Browse page, UniGene: Hs.00000 on the Report page), go to UniGene to identify STSs with sequence in a cluster.
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How can I get from a locus record to maps that contain this gene?
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In the browse lists for the human, mouse, and Drosophila genomes, the Position column provides a link to an appropriate Map Viewer page. There the Display settings function can be used to control the maps and regions to be included. Also, if a UniGene link is displayed (UniGene: Hs.00000 on the Report page), try UniGene to determine whether there are STS mapping data on radiation hybrid panels. Or if an OMIM link is displayed ( on the browse list, OMIM: 000000 on the Report page), go to OMIM to determine whether a Gene Map record exists. From the Report pages, the link mv generates a query to NCBI's Map View to display maps available for that genome. For the rat and zebrafish genomes, more map information may be found from the appropriate genome-specific database.
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How are links between UniGene and LocusLink computed?
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UniGene<->LocusLink connections are computed based on sequences curated to represent a locus by LocusLink/RefSeq collaborators and clustered by UniGene. If the LocusLink/RefSeq curation process identifies multiple accessions as valid for a gene, then these are constrained to be in the same UniGene cluster. Our goal is to improve the correspondence between UniGene and LocusLink such that for any gene anchored with sequence data, there is a single UniGene cluster.
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What if I know the Accession number for a gene for which LocusLink displays
no Accession number? How can I correct this omission?
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We encourage your suggestions. Please email to the NCBI Service Desk and provide your name and contact information, the accession number, and the LocusID to which you believe the sequence corresponds.
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I know there are more sequence Accession numbers for a gene or protein than what I see listed. Why?
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LocusLink is not designed to report Accession numbers
for all published sequences from a given gene or protein. The goal is to
provide a set of sequences known to be representative. Other tools such as Entrez
"related sequences" or BLAST, or BLink
can be used to retrieve more records. The number and specific instances of the
Accession numbers that are reported depend on whether the gene has a
provisional or a reviewed RefSeq record, or no RefSeq record at all.
- If there is no RefSeq record, each Accession number is one suggested to represent the gene, but no tools have been used to identify other related sequences.
- If the RefSeq record is in the provisional category, additional records annotated with complete coding regions, which do not exceed a cutoff nucleotide mismatch level, are listed.
- If reviewed, the sequences used to generate the sequence "assembly" are reported explicitly. Other GenBank records that represent this gene are also listed; but again, this list is not comprehensive.
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How can I convert a list of Accession numbers into LocusID values?
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One approach for converting Accession numbers to LocusID values is to use the file ftp://ftp.ncbi.nih.gov/refseq/LocusLink/loc2acc. This file, updated daily, contains the values documented in ftp://ftp.ncbi.nih.gov/refseq/LocusLink/README.
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How often is LocusLink updated?
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The files are usually updated weekly, over a weekend. The statistics pages will provide the last date the files were refreshed.
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How are symbols and gene names selected for LocusLink and RefSeq records?
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Both LocusLink and RefSeq use gene symbols and
gene names established by the nomenclature committee
appropriate for the genome. In a LocusLink report, that symbol and name is reported under the banner Official Gene Symbol and Name. In a RefSeq record, the symbol is reported as the LOCUS and as the feature gene=, and the name is used in the DEFINITION.
If an official symbol has not yet been assigned, then an interim symbol and name are arbitrarily selected by any of our collaborators.
Alternate symbols and names are added by collaborators and during the analysis that accompanies making a reviewed RefSeq record.
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Which citations are selected for LocusLink reports and RefSeq records?
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Explicit links to citations via PubMed are selected by our collaborators, for the human this corresponds primarily to the Human Gene Nomenclature Committee and Online Mendelian Inheritance in Man (OMIM). These citations usually report gene discovery and mapping. Some citations documenting function and and expression of a gene and its products are also added during the analysis that accompanies making a reviewed RefSeq record, or as part of other annotation processes.
LocusLink reports and RefSeq records are not intended to report all citations associated with a gene or its protein products. The goal is to
provide a set of citations that provide some background information. Either these citations, or those included in linked OMIM reports, can then be used to find related publications by such tools as PubMed's Related Articles.
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