Expedited access to some of CottonDB's most Frequently Asked
Queries.
We'd like to have all the CottonDB FAQs available right
here.
** You can help! **
If you have a CottonDB question you want to ask, please
let me know. Somebody else probably has the same question.
- Jing, jingyu@tamu.edu
Germplasm
-
Gossypium Species Summaries
: a table matrix of species names and genome, haploid chromosome number, geographic
origin, and number of accessions held, number of sequences, and number of DNA libraries currently
available in CottonDB.
--- Suggested by: Sarah Palmer ---
- Germplasm Trait Evaluation Information
[View trait descriptions]
- List Germplasm by Collection Groups
- List germplasm whose pedigree includes a certain germplasm.
- Germplasm Passport Information, search by country of origin (* for all).
Markers and Maps
- Map
Data Summaries lists species, genome; mapping population
parents, type, and size; number of loci; references and contact person for each
map currently available in CottonDB.
- Mapped
Sequences, with information of mapping position.
--- Suggested by: Cairui Lu ---
- Nearby Loci: A list of all Loci that are within a specified distance
of a specified Locus on any map.
- Map Positions, by marker type: Select a marker type to see a list
of loci and mapping positions.
Primers and Probes
- SSR primers and mapping information.: Select a microsatellite set
and the type of information you would like to view.
- SSR
Polymorphisms: A list of primer names, allele sizes,
germplasm names, germplasm cottondb_id, and species names.
References
- Find references within a certain time period. (Keyword can be left blank).
- Search by author, keyword and/or date. (Author and Keyword
can be left blank. "since" must be a number.)
Sequences and DNA Libraries
- DNA
Library summaries: a list of libraries including information on source
species, source germplasm, source tissue, contact person, and the number of
sequences derived from the library and currently available in CottonDB.
Variety Test Reports
Nomenclatures
- Chromosome Names of tetraploid
cotton: A table of proposed and formerly assigned At- and Dt-genome
chromosomes, with mapped sequence information.
- Germplasm Primary Names are chosen from the multi-names and
identifiers associated with each germplasm record.
Currently only data records that are within data sets of NPGS Cotton Plant Variety
Protection (USA), NPGS Crop Science Registration (USA), Pedigrees of Upland
and Pima Cultivars, plus a few germplasm records from public reports have Primary names.
Inputs from germplsm experts are needed to establish appropriate primary names for
records that currently use cottondb_id as their primary name. However, query can be made
on any identifier in the germplasm record. Primary
Name Table lists germplasm primary names with all other names and identifiers that
have been used in data records.
- Map Names of AD genome genetic maps are assigned using an "A-B_C/D" system,
where A = initials of the two parents of the mapping population; B = population type;
C = chr + chromosome number; D = linkage group name or A or D tetraploid name.
- Reference Names in CottonDB are assigned using an "A-B-C" system, where
A = journal code; B = journal volume number; C = starting page number of the
article. Reference
Name Table lists Journal codes, journal names, the number of articles that currently
in CottonDB, and other information about the journal.
- Universal Names are used to make connections among Locus, Primer, Probe, Sequence, Clone, etc.,
and were chosen based on primer or probe names. Universal
Name Table lists universal names with names that are used in
different data classes.
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