MMP Downloads

2004-09-27
- BAC - Marker association file for AGI (cumulative) -- updated 2004-09-27
- agi20040927.txt.gz 3.7 mb gzipped text file
- agi20040927.txt 35 mb text file caution!
- format is as in previous file:
  bac name:MARKER:fpctype:physical probe id:physical probe name:genetic probe id:genetic probe name:locus id:locus name:chromosome:bin:ibm coordinate:framework:map quality:gramene id:genbank accession:data provider
- note: updates include new genetic markers included on the IBM2 2004 neighbors maps, in particular new SNP's (Mike McMullen) and RFLPs (Genoplante) designed from sequences associated with overgo physical probes.
- markers20040713.txt. A file of relationships of the various physical markers to genetically mapped markers.
2004-07-13
- BAC - Marker association file for AGI (cumulative) -- updated 2004-07-13
- agi20040713.out.gz 3.5 mb gzipped text file
- agi20040713.out 22.8 mb text file caution!
- format is as in previous file:
  bac name:MARKER:fpctype:physical probe id:physical probe name:genetic probe id:genetic probe name:locus id:locus name:chromosome:bin:ibm coordinate:framework:map quality:gramene id:genbank accession:data provider
- note: updates include new and revised bac-physical probe (overgo) data from Andrew Paterson; some genbank accessions are revised
- Also, the MARKER field is now the same as the physical probe name.
- Also, all physical and genetic probe names agree with MaizeGDB, for example SSR 'umc1200', in previous file, is now 'p-umc1200'
- Map quality indicators 1, 2 indicate very close, or identical relationship of the genetic and physical map probes. Map quality 3, is less certain.
- markers20040713.txt. A file of relationships of the various physical markers to genetically mapped markers.
2003-08-19
- BAC - Marker association file for AGI (cumulative) -- updated 2003-08-19
- agi20030819.out.gz 3.9 mb gzipped text file
- agi20030819.out 18.3 mb text file caution!
- format is:
  bac name:MARKER:fpctype:physical probe id:physical probe name:genetic probe id:genetic probe name:locus id:locus name:chromosome:bin:ibm coordinate:framework:map quality:gramene id:genbank accession:data provider
- note: NEW FORMAT!!!. Updated to include newer IBM2 Neighbors map data and to include a map quality indicator.
- Also to include the new MARKER field which is the name for use in designating that particular marker.
- Also includes a letter designation for some MARKER names when a particular marker hits one of several BAC groups
2003-07-02
- BAC - Marker association file for AGI (cumulative) -- updated 2003-07-02
- agi20030702.out.gz 3.4 mb gzipped text file
- agi20030702.out 15.5 mb text file caution!
- format is:
  bac name:fpctype:physical probe id:physical probe name:genetic probe id:genetic probe name:locus id:locus name:chromosome:bin:ibm coordinate:framework:map quality:gramene id:genbank accession:data provider
- note: NEW FORMAT!!!. Updated to include newer IBM2 Neighbors map data and to include a map quality indicator.
2003-04-14
- BAC - Marker association file for AGI (cumulative) -- updated 2003-04-14
- agi20030414.out.gz 1.5 mb gzipped text file
- agi20030414.out 13.2 mb text file caution!
- format is:
  maizedb:bac:marker:fpctype:chromosome:ibm coordinate:framework:gramene id:genbank accession:data provider
- note: updated to REMOVE IBM2 Neighbors map data for overgo markers placed there in silico.
2003-04-04
- BAC - Marker association file for AGI (cumulative) -- updated 2003-03-27
- agi20030327.out.gz 1.5 mb gzipped text file
- agi20030327.out 13.4 mb text file caution!
- format is:
  maizedb:bac:marker:fpctype:chromosome:ibm coordinate:framework:gramene id:genbank accession:data provider
- note: updated to include the latest set of Bac pool PCR data.
- BAC - Marker association file for AGI (only the NEW data) -- updated 2003-03-27
- agi20030327new.out.gz 13 kb gzipped text file
- agi20030327new.out 85 kb text file
- format is:
  maizedb:bac:marker:fpctype:chromosome:ibm coordinate:framework:gramene id:genbank accession:data provider
- note: this is the data from the latest set of Bac pool PCR data.
2003-03-11
- BAC - Marker association file for AGI -- updated 2003-03-11
- agi20030311.out.gz 2.2 mb gzipped text file
- agi20030311.out 13.4 mb text file caution!
- format is:
  maizedb:bac:marker:fpctype:chromosome:ibm coordinate:framework:gramene id:genbank accession:data provider
- note: updated to include the second to the last set of Bac pool SSR-Primer data.
- note: updated to include chromosome, coordinate and framework information as based on the IBM2 Neighbors map.
- note: framework field defined as follows: 1 = on-frame 0 = off-frame
- note: marker names have been updated for Cornsensus-derived overgos to reflect the difference between the overgo probes and the actual unigenes
- IBM2 and IBM2 Neighbors Genetic Map file for AGI manual editors -- updated 2003-03-11
- ibm_genetic_map.out 450 kb tab delimited text file
- IBM_Genetic_Map.xls 1.1 mb Excel file
- format is:
  probe id, probe name, probe type, locus id, locus name, locus type, IBM2 chromosome, IBM2 backbone, IBM2 coordinate, IBM2 Neighbors chromosome, IBM2 Neighbors backbone, IBM2 Neighbors coordinate
2002-10-30
- BAC - Marker association file for AGI/CUGI -- updated 2002-10-30
- agi20021030.out.gz 2.2 mb gzipped text file
- agi20021030.out.tgz 2.2 mb gzip'd & tar'd text file
- format is:
  maizedb:bac:marker:fpctype:chromosome:ibm coordinate:gramene id:genbank accession
- note: updated to include anonymous DuPont overgos and latest Bac pool SSR-Primer data.
2002-10-07
- in silico association file for all Zea mays sequence (in GenBank by 2002-10-7) with the Cornsensus unigene set
- zeamays_vs_cornsensus_20021007.out 52.1 mb text file
- format is tab-delimited with the following columns:
  blast_prog, blast_db, query_def, query_length, iteration_num, hit_num, hit_def, hit_length, hsp_num, hsp_bitscore, hsp_score, hsp_evalue, hsp_alignlen
2002-09-28
- in silico association file for all Zea mays probes with sequence information with the BACs and Contigs (FPC from 2002-9-28)
- insilico_probe_ctg_20020928.out 2.3 mb text file
- format is tab-delimited with the following columns: (note: -1 in ibm or ibmn indicates LACK of presence on that map)
  probe_id, probe_name, probe_type, locus_id, locus_name, chromosome, ibm, ibmn, cornsensus_name, bac_name, contig_name
2002-09-24
- in silico association file for all Zea mays probes with sequence information with the BACs (2002-9-24)
- blast_associations_20020924.out 3.4 mb text file
- format is tab-delimited with the following columns: (note: -1 in ibm or ibmn indicates LACK of presence on that map)
  probe_id, probe_name, probe_type, locus_id, locus_name, chromosome, ibm, ibmn, cornsensus_name, bac_name
2002-09-19
- BAC - Marker association file for AGI/CUGI -- updated 2002-09-19
- cugi20020919.out 9.4 mb text file
- cugi20020919.out.tgz 1.9 mb tar gzipped file
- cugi20020919new.out 67 kb text file (only the new data)
- note: the tar gzipped file should result in a file save box depending on your mime-type settings
- format is:
  maizedb:bac:marker:fpctype:chromosome:ibm coordinate:gramene id:genbank accession
2002-08-14
- BAC - Marker association file for AGI/CUGI -- updated 2002-08-14
- cugi20020814.out 9.3 mb text file
- cugi20020814.out.tgz 1.9 mb tar gzipped file
- note: the tar gzipped file should result in a file save box depending on your mime-type settings
- format is:
  maizedb:bac:marker:fpctype:chromosome:ibm coordinate:gramene id:genbank accession