Timing results for building a singleTCW database.

1<p>The plantTFDB database, the SwissProt and TrEMBL taxonomic databases for plants, invertebrates, fungi, viruses, vertebrate and a subset of the complete UniProt (i.e. minus the sequences from the bacteria and these 5 taxonomic databases). This is based on the April 2012 UniProt, where this set of databases (plus bacteria) take about 45G disk space.</p

The viewMultiTCW interface.

<p>This shows the table of orthoMCL inflation 4.0 clusters where there is at least one sequence from each species. The H-ID and H-Desc columns are the annotation hit that the majority of the sequences have, e.g. for cluster OM4_0001010, 100% have the hit PXM16_ARATH where the best of them has an e-value of 0.0. The columns can be changed by selecting the “Select Columns” at the bottom, which will immediately change the table (i.e. a new search of the database is not required).</p

Timing results for building a multiTCW database from 4 singleTCW databases.

1<p>ESTscan does not produce protein sequences for all transcripts.</p

The viewSingleTCW interface.

<p>This shows the main table, where the filter was set to show all sequences where tip is differentially expressed compared to root and stem using a 1E-10 cutoff. The columns are: Root, Stem and Tip are the RPKM values; TiRo and TiSt are DE p-values between tip-root and tip-stem, respectively; BestAnno (AN) is the best annotation for the sequence (i.e. not containing phrases such as “uncharacterized protein”); and the last four columns are the BestAnno description, BLAST e-value, the DB type (‘tr’ = TrEMBL, ‘sp’ = Swiss-Prot, ‘TF’ = plantTFDB), and the taxonomic type (all these best hits are from plants).</p

The runDE interface.

<p>This shows the setup to compute the differential expression (DE) between tip and root using the edgeR method with default normalization. The results will be written into a database column called “TiRo”. Once all DE values are computed, the “All Pval Columns” can be selected followed by “Execute GOSeq” to compute the corresponding GO differential expression p-values.</p

The runMultiTCW interface.

<p>This shows the configuration for building a comparison multiTCW database of 4 rhizome singleTCW databases. Three cluster methods were performed: orthoMCL with inflation 1.5, orthoMCL with inflation 4, and transitive with 80% similarity and 80% overlap. The italicized methods indicate they have been added to the database; new clusters can be added and will not be italicized until processed.</p

SyMAP view of unedited physical maps of chromosome 1 from eight diploid species aligned to the ssp

chromosome 1 RefSeq. The numbers in the small rectangles on the left are contig numbers of OMAP phase I physical maps. Beige bars on the right represent the RefSeq (IRGSP V.4 assembly) and the red crosses on the beige bars represent the CentO position of [18]. Purple lines represent BESs aligned to the RefSeq. The order of the species from the left to right is; [AA], [AA], [AA], [BB]; [CC], [EE]; [FF], [GG].<p><b>Copyright information:</b></p><p>Taken from "Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus "</p><p>http://genomebiology.com/2008/9/2/R45</p><p>Genome Biology 2008;9(2):R45-R45.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2374706.</p><p></p