Query reg Phylo tree

[rosh...@ncbs.res.in]

Dear Sir/ Madam

I am studying an lncRNA transcribed from the intron of a protein coding gene.

I used UCSC genome browser to examine its conservation across phyla and
also to create a phylogenetic tree; images attached herewith.

Surprizingly, even though the sequence is conserved only in mammals and
absent in lower organisms, the phylo tree still includes lower organisms
like chicken, zebra fish etc as well.

I shall be very grateful to you if you could kindly explain this to me.

Thanking you,

sincerely,

Dr. Roshan Fatima
National Center for biological sciences (NCBS)
Bangalore
India
560065

[Cath Tyner]

Hello Roshan,

In order to best support you, would you be willing to help me replicate your results? There are two ways you can do this.

1. You can simply save a session and reply to me (ca...@ucsc.edu) with your session link.

To save a session, simply configure the browser to the display that you want to save.

Then, click on "My Data" > "My Sessions" 

Under "Save Settings" enter a name for session with the checkbox marked, "allow session to be loaded by others."

Then you select the "Email" link in the sessions table list to email it to me. 

2. You can list the steps that you took so that I can replicate your results, including the lncRNA you are interested in. It would also be helpful to include screen shots of the settings page for your conservation track. 

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Cath Tyner]

Hello again Roshan,

I also meant to let you know that you will need to configure the tree to meet your specifications. The tree branching does not automatically configure based on other track settings, it is an independent tool. In the "Notes" section of the page (https://genome.ucsc.edu/cgi-bin/phyloGif) you can see examples of how to build the tree. 

Please respond to this forum if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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​Enjoy,​

Cath

. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser