User GenomeMark to bookmark regions in genome browser
From Array Suite Wiki
GenomeMark is a bookmark-like utility in genome browser. Adding regions into genomemark will record genomic regions. User can jump back to marked regions by a single click on the genomemark.
There are several ways to add genomemarks. By default, there are two genomemark categories: SequenceMatch and CustomRegion.
In Omicsoft Genome browser, user can search a piece of DNA, RNA and protein sequence in the current browser. If the search function finds a mapped location, the genome browser will jump to the region and the region will add into genomemark as YourSeq. If user searched multiple times, regions are marked as YourSeq1, YourSeq2, ..., YourSeqN. Sequence search results are marked in SequenceMatch category.
In particular, the Protein Sequence Search function searches the query Amino Acid sequence against the protein collection in the first loaded gene model in a genome browser. The query sequence requires at least 3 amino acids, and supports regular expression (e.g. use “.” to represent any amino acid). The search results will be the exact match of the query string in the gene model that was first loaded in a browser.
If user navigates into a region of interest and want to mark the region, he/she can click the "favorite" button on top. A custom region window will pop up and user can add name, tag and description for this region. It will shown up in CustomRegion category in genomemark.
User can import genomeMark to genome browser just as we can import web browser bookmarks. User can import the interesting genomeMark using Files | Import Custom Regions. User can import files in one of the following formats:
- Binary Custom Region Files (.bcr)
- Bed file (.bed)- http://useast.ensembl.org/info/website/upload/bed.html
- Region list (.txt) - A list of regions defined by Chromosome, Start and End.
- Gene list (.txt) - A list of gene symbols, one gene on each row.