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Fourth, current unigenic evolution analyses treat the mutagenic PCR protocol as a 'black box' process that takes a wild-type sequence as input and produces a pool of mutagenized clones as output.

We sequenced 53 clones from the output of round 5 to determine the sequence changes that led to the improved binding in the presence of GuHCl.

A second script was developed to compare the *.gff files of either of the two mutant clones against the output obtained for AS-sens.

Therefore, since kinases and phosphatases are involved in biochemical and cell-cycle pathways essential for proliferation and cell survival, the long-term selection method could have eliminated the less viable clones from the final output.

Analyses of approximately 20% of the genome following cloning and sequencing of output populations clearly demonstrate a significant positive correlation between MOI and multiple measures of genetic diversity.

To obtain a non-redundant set of transcripts, we clustered 5′ or 3′ end sequences according to clone names in the CAP3 output.

The clone deconvolution module generates as output a summary file, an anchored positive marker file used for convenient conversion to an ACE file to merge markers into a FPC contig map, and a deconvolution result file for each marker for further manipulation.

It returns an output showing whether the clone is the expected one, and if not what the clone is most likely to be.

Single clones reisolated after plating the output samples were used.

A total of 6 12 phage clones were sequenced from the output of each group in rounds 3 5 using established colony PCR-based protocol.

Raw-intensity hybridization outputs for each clone before and after MSRE treatment were genotyped using the Dynamic Model Mapping Analysis (GCOS/GDAS software package; Affymertrix) or, for raw intensity analysis, normalized and compared with a pool of 13 genomic DNA samples from pedigrees 1332 and 45 using the dChip copy number analysis tool http://www.dchip.org.

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