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

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Presentation transcript:

ID Mapping to accessions from different databases. COST Functional Modeling Workshop April, Helsinki

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).

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

1.UniProt ID Mapping

Paste accession list (>1000 may cause errors).

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

The mapping link will display a tab separated file:

2. Ensembl BioMart

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

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

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

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

3. g:convert This tool works for all Ensembl species.

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

4. AgBase: ArrayIDer bin/tools/arrayider_select.pl Maps ESTs to gene/protein accessions.

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

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: