1. ID Mapping to accessions from different databases. COST Functional Modeling Workshop 22-24 April, Helsinki

2. Converting Database Accessions  May quite frequently need to convert between database accessions when doing functional modeling.  Always check what accessions the tools you plan to use accept.  Not all accessions can be converted to all other accessions (data loss).  If you have a choice, use the accession type that matches most of you data.  Plan your tool use to ensure you do less accession conversions (minimize data loss).

3. Converting Accessions Examples 1. UniProt database 2. Ensembl BioMart 3. Online analysis tools  g:profiler’s g:convert program 4. AgBase database  ArrayIDer tool

4. 1.UniProt ID Mapping http://www.uniprot.org

5. Paste accession list (>1000 may cause errors).

6. Select the accession type you have: and the accession type you want to convert to: Click an MAP

7. The mapping link will display a tab separated file:

8. 2. Ensembl BioMart http://www.ensembl.org

10. Clicking on these headings allows you to set up searches. Selecting FILTERS gives you different filtering options:

11. Expand GENE and check “ID list limit” to select a defined list of accessions. Enter your list of accessions.

12. Selecting ATTRIBUTES allows you to choose what information is reported: Check accessions from external databases (UniProt & RefSeq).

13. Clicking on RESULTS will show you the output information. Output can be displayed online and/or downloaded (text, Excel). Selecting FILTERS or ATTRIBUTES will allow you to go back and make changes. Limited to species represented in Ensembl

14. 3. g:convert http://biit.cs.ut.ee/gprofiler/gconvert.cgi This tool works for all Ensembl species.

16. g:convert contains Ensembl genomes data works from a very large range of accessions (including array IDs) can also collect genes based upon Ens chromosomal locations Online help, tutorials & support last updated Jan 2013

17. 4. AgBase: ArrayIDer http://www.agbase.msstate.edu/cgi- bin/tools/arrayider_select.pl Maps ESTs to gene/protein accessions.

20. An email will be sent with a link to the results. Results are formatted as an Excel file.

21. Combining ID Mapping  If you have mixed accession types, you may have to do your ID mapping in sections and link together the results.  Most mappings are not 100% - need to note how many from your original dataset are available for further analysis.  For more help with accession mapping, contact AgBase: agbase@hpc.msstate.edu