Research article
Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation
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* Corresponding author: Ian Armstead ian.armstead@bbsrc.ac.uk
Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
BMC Genomics 2007, 8:283 doi:10.1186/1471-2164-8-283
Published: 20 August 2007Additional files
Additional file 2:
Contains supplementary tables: Additional file 2 Table 1 details the %MegaBLAST alignments between the different TRL categories in the Os_CD database and the other plant databases. Additional file 2 Table 2 details the % MegaBLAST alignments and average scores of linear 10% segments of FAexpTRL for each pseudomolecule for each plant database. Additional file 2 Table 3 details the relation between colour codes used in the MW displays and the distribution of percentage alignments, average scores, segmentally duplicated FAexpTRL and gene family sizes. Additional file 2 Table 4 details derived gene family sizes used in the calculation of MWs for gene family size.
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Additional file 3:
Illustrates the %MegaBLAST alignments/rice pseudomolecule between FAexpTRL and the plant databases.
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Additional file 7:
Lists moving window (MW) scores used to produce Figures 3, 4 and Additional file 4.
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Additional file 1:
Supplementary methods describing the derivation of FAexp gene family sizes based upon identical annotations.
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Additional file 4:
Illustrates colour coded MWs comparing %alignments between the Os_CD database and the test databases in relation to average gene family size.
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Additional file 6:
Lists 1)TIGR rice loci model identifiers and annotation categories; 2) Arabidopsis gene models used in MegaBLAST analyses; 3) TIGR rice loci gene families and sizes based upon identical annotations.
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Additional file 5:
Contains MegaBLAST scores for the test databases against Os_CD.
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