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资源说明：Code to handle aligning sequences to the potato genome, including 454 paired-end sequences and various 'mate pair' sequences from BACs, fosmids, and tomato clones.
Clone_Ends
PE/MP aligned to potato assembly 3
* ASSEMBLY = Assembly/PGSC0003DM/PGSC0003DMB.fa
* DM_BES = LIBGSS_011841 Solanum phureja POTATO-B-01-100-110KB
* DM_FOS = LIBGSS_011804 Solanum phureja POTATO-F-01-40KB
* RH_BES = LIBGSS_010743 Solanum tuberosum RHPOTKEY BAC ends
* SL_BES = Various Solanum Lycopersicum
PIPELINE:
1) Alignment is done with SSAHA2, using the default 'Sanger' hashing
and matching aoptions.
2) The 'raw' SSAHA2 output is filtered using the 'depth_filter.plx'
Perl script using a coverage (-c) of 0.8 and a depth (-d) of 3.
3) The 'raw GFF' is generated directly from the filtered SSAHA2
alignment results using the 'ssaha_to_gff.plx' Perl script.
4) The 'paired GFF' is generated using the 'raw GFF' and a
bambus-style 'mates' file using the 'to_gff.plx' Perl script.
5) The 'paired GFF' is loaded into GBrowse, and is visualized using
the 'clone.conf' GB Perl-style configuration
References:
DM_BES:
A BAC library was constructed by Lucigen from Solanum phureja DM1-3
516R44 (CIP801092). End sequences were generated using primers in the
vector (pSMART) using Sanger sequencing at the J Craig Venter
Institute. All sequences are in GenBank (Accession numbers GS025504
...). A total of 156,485 sequences are found in this file.
CITATIONS
Title: Sequencing of the Solanum phureja doubled monoploid clone,
DM1-3 516R44 (CIP801092)
Authors: Buell,C.R., Lundback,S.S.
Year: 2009
Status: Unpublished
DM_FOS:
A fosmid library (40 kb insert sizes) was constructed from Solanum
phureja DM1-3 516R44 (CIP801092). End sequences were generated using
primers in the vector (pCC1FOS) using Sanger sequencing at the J Craig
Venter Institute. All sequences are in GenBank (Accession numbers
FI900795-FI901529, FI907952-FI927051, GS557234-GS594339,
GS635316-GS765760). A total of 187,386 sequences are found in this
file.
CITATIONS
Title: Sequencing of the S. phureja doubled monoploid clone, DM1-3
516R44 (CIP801092)
Authors: Buell,C.R., Lundback,S.S.
Year: 2009
Status: Unpublished
RH_BES:
A BAC library (library name RHPOTKEY) was constructed by Keygene from
Solanum tuberosum clone RH89-039-16. The library comprises a mixture
of EcoRI and HindIII partial digest genomic DNA fragemnts. End
sequences were generated using primers in the vector (pIndigoBAC-5)
using Sanger sequencing at the J Craig Venter Institute. All sequences
are in GenBank (Accession numbers EI367122-EI391525,
EI812397-EI846477, ER788642-ER870415). A total of 140,259 sequences
are found in this file.
CITATIONS
PubMed ID: 18554403 http://www.ncbi.nlm.nih.gov/pubmed/18554403
Title: Analysis of 90 Mb of the potato genome reveals conservation
of gene structures and order with tomato but divergence in
repetitive sequence composition
Authors: Zhu,W., Ouyang,S., Iovene,M., O'Brien,K., Vuong,H., Jiang,J.,
Buell,C.R.
Citation: BMC Genomics 9 (1): 286 2008
SL_BES:
See...
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