User GenomeMark to bookmark regions in genome browser

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GenomeMark

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.

Sequence search

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.

20130423 GenomeMark1.png


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.

ProteinSequenceSearch1.png

Custom Region

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.

20130423 GenomeMark2.png

Import 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:

User can also add more complicated GenomeMark using Add Track | Genomemark track: tab delimited file. Here is one example using a test file [1].

20130423 GenomeMark3.png