UCbase 2.0 on-line help

Center for Genome Research

University of Modena and Reggio Emilia

Italy

Last update: April 3rd, 2014

Introduction

Improvements over our previous version of UCbase include searching tools for UCR Id, Gene,Pathology and sequence. In particular, it is possible to visu- alize if the genes in which UCRs are located have SNPs, splicing events or if they are involved in specific pathologies. To interrogate UCbase for genetic or non-genetic disorders, we have chosen to use the standardised Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT). SNOMED CT is a systematic, computer-processable collection of medical terms, in human and veterinary medicine that provides codes, terms, synonyms and definitions that cover anatomy and diseases. It allows a consistent way to index, store, retrieve, and aggregate medical data across specialties and sites of care. New features include also a query to search for specific SNPs using dbSNP Ids. The results show the UCRs located within the gene that has that specific SNP or mutation together with chromosomal coordinates, allelic frequency, validation and phenotype information. Moreover, the new BLAST query al- lows to match a sequence against the entire UCRs sequence database and includes now a tool that gives the opportunity to filter the results for UCRs located in genes or chromosome regions involved in specific pathologies.

1. Search for UCRs by Id

UCRs are 481 sequences annotated by numbers: uc1, uc2, uc3, etc. Thus they can be searched by their Ids. UCRs are 481 sequences annotated by numbers: uc1, uc2, uc3, etc. It is also possible to search for many UCRs simultaneously clicking on the UCR Id and the ctrl (for Windows users) or cmd (for Mac users) button. Thus they can be searched by their Ids and other information such as:

- Chromosome coordinates (Chr, Start, End, Strand, type*)
- ENSEMBL Gene Id
- Gene Symbol
- SNPs (located within or 500bp up/downstream a specific UCR). SNPs located inside (within) the UCRs are always shown at the top of the table.
- Alternative Splicing sites
- Pathology

*In field type "e" is exonic, "n" is non-exonic and "p" is possibly exonic.

2. Search for UCRs by SNPs

New features include also a query to search for specific SNPs using dbSNP Ids (http://www.ncbi.nlm.nih.gov/SNP/). A search for a specific SNP returns all UCRs in which the polymorphism is located (within or 500bp upstream/downstream a specific UCR) together with chromosomal coordinates, allelic frequency, validation, and phenotype information.

3. Search for UCRs by Genes

UCRs can be retrieved also by searching for the genes in which they are located. “Hugo Gene Symbol” nomenclature has been used to annotate these genes. In particular, it is possible to visualize if these genes have SNPs, splicing events or if they are involved in specific pathologies.

4. Search for UCRs by Pathologies

To interrogate UCbase for genetic or non-genetic disorders, we have chosen to use the standardised Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT). SNOMED CT is a systematic, computer-processable collection of medical terms, in human and veterinary medicine that provides codes, terms, synonyms and definitions that cover anatomy and diseases. It allows a consistent way to index, store, retrieve, and aggregate medical data across specialties and sites of care.

5. Search for UCRs by Chromosome Coordinates

UCRs information can be retrieved giving the chromosome number, and the chromosome coordinates for a specific genomic region.

6. Match your sequence vs UCRs

The new BLAST query allows to match a sequence against the entire UCRs sequence database.

6.1 Filter for Pathology

UCbase includes now a tool that gives the opportunity to filter the results for UCRs located in genes or chromosome regions involved in specific pathologies.

7. Type your own query

This tool is dedicated to bioinformaticians who prefer to directly interrogate our database using MySQL language (www.mysql.org). The database scheme is shown in our data mining web page.

For details please download the manual at www.dsb.unimo.it/UCbase/help/help.pdf

Contacts

CGR - CENTER FOR GENOME RESEARCH - UNIVERSITY OF MODENA AND REGGIO EMILIA
CGR is one of the most important center for Genome Research in Italy. Our work is main focused on Next Generation Sequencing Analysis. Visit CGR website at http://www.cgr.unimore.it

INFORMATION SYSTEMS GROUP - UNIVERSITY OF MODENA AND REGGIO EMILIA
The work of the ISGroup, here at the Computer Engineering Department (DII) of the University of Modena and Reggio Emilia, mainly focuses on the design and development of new systems, algorithms and data structures for the access and management of Information. Visit ISGroup website at http://www.isgroup.unimo.it

Email: ucbase@unimore.it