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Suppressive Subtractive Hybridization

Whole genome sequencing is too cost-prohibitive for many investigators to use it to obtain sequence data for multiple strains of the same microbe or for related species. One alternative, more cost-effective method of examining gene diversity and genome plasticity among related microbes is subtractive hybridization (SH).

A variation of this method, suppressive subtractive hybridization (SSH), was developed by CLONTECH and kits have been optimized for use with genomic DNA (the PCR-Select Bacterial Genome Subtraction Kit) and cDNA (the PCR-Select cDNA Subtraction Kit) (description of technology).

Clones resulting from SSH are end sequenced, and the resulting sequences are either assembled (if they overlap) or joined with a linker. These 'assemblies' are searched for protein sequences using BLASTX and TIGRs non-redundant protein database. Open reading frames are identified and annotated. The assemblies and annotation are presented here.

Current Experiments

Experiment

# clones

# sequences

# contigs

# of genes

F. intestinalis (F. succinogenes)

1056

1879

712

502

R. flavefaciens FD-1 (R. flavefaciens JM1)

381

328

233

Total

1437

1879

1040

735

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