failed query: select si.study_id, si.study_name, count(csl.clone_id) from study_info si, clone_study_link csl where csl.study_id=si.study_id group by si.study_id Server message number=208 severity=16 state=1 line=1 text=study_info not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=clone_study_link not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). failed query: select csl.study_id, count(al.seq_name) from clone_study_link csl, clone_description cd, stan s, asmbl_link al where iscurrent=1 and al.asmbl_id=s.asmbl_id and al.clone_name=cd.clone_accession and cd.clone_id=csl.clone_id group by csl.study_id Server message number=208 severity=16 state=1 line=1 text=clone_study_link not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=clone_description not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=stan not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=asmbl_link not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). failed query: select csl.study_id, count(distinct adcl.asmbl_data_id) from stan s, asmbl_data_clone_link adcl, clone_study_link csl where csl.clone_id=adcl.clone_id and s.asmbl_data_id=adcl.asmbl_data_id and s.iscurrent=1 group by csl.study_id Server message number=208 severity=16 state=1 line=1 text=stan not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=asmbl_data_clone_link not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=clone_study_link not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). failed query: select csl.study_id, count(distinct f.feat_name) from stan s, asm_feature f, asmbl_data_clone_link adcl, clone_study_link csl where s.iscurrent=1 and f.asmbl_id=s.asmbl_id and f.feat_type="ORF" and adcl.asmbl_data_id=s.asmbl_data_id and csl.clone_id=adcl.clone_id group by csl.study_id Server message number=208 severity=16 state=1 line=1 text=stan not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=asm_feature not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=asmbl_data_clone_link not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Server message number=208 severity=16 state=1 line=1 text=clone_study_link not found. Specify owner.objectname or use sp_help to check whether the object exists (sp_help may produce lots of output). Suppressive Subtractive Hybridization - Rumenomics - JCVI
 
 
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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.

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