Orthologs between hg19 and rn4

[Aishwarya Kulkarni]

Hi,

I am trying to identify the conserved binding sites of a protein between humans and rats and after reading lot of the discussion topics , I am wondering if using net files would be the best option i.e the one located here:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/vsRn4/ , if so how would I use it on the command prompt and what would be the best way to validate the orthologous (hence conserved) between humans and rats,

Thanks

Aishwarya

[Brian Lee]

Hi Aishwarya,

Thank you for using the UCSC Genome Browser and your question about identifying conserved binding sites of a protein between humans and rats.

Rather than the net files, you should likely look at the chain link table, hg19.rn4.all.chain.gz, which would identify the corresponding sequence in the other species. Here is a link with information about the chain format, http://genome.ucsc.edu/goldenPath/help/chain.html, and for comparison the page about the net format: http://genome.ucsc.edu/goldenPath/help/net.html

The chain format is deliberately quite dense where an initial header line starts a section followed by alignment data lines which represent the size of ungapped alignments and difference between block sizes. Here are some example lines from hg19.rn4.all.chain.gz:

chain 578869426 chr14 107349540 + 25151529 106332175 chr6 147636619 + 64051113 138454126 1
17 2 0
57 0 1
21 2 0
4 4 0
...

You could also examine the reciprocal best file for a more filtered answer. Ordinary liftOver chains are not necessarily equivalent in both directions, while the filtered reciprocal best chains are generated for that purpose. A reciprocal best chain exists for rn6:http://hgdownload.soe.ucsc.edu/goldenPath/hg19/vsRn6/reciprocalBest/ but not for rn4. Here are some example lines from hg19.rn6.rbest.chain.gz (note new rn6 chr6 coordinates mapping from the same hg19 region on chr14):

chain 567867938 chr14 107349540 + 25151529 106332175 chr6 147991367 + 64895805 138251111 1
17 2 0
57 0 1
21 2 0
...

Please know we have mailing list archives you can search to find answers that might be of interest. For example some previous answers point users on how to build reciprocal best chains: https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/reciprocal$20best

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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[aishwarya kulkarni]

Hi Brian,

How are the rbest files to be used after they are generated on the coordinates that I am interested in?

Aishwarya.S.Kulkarni

[Christopher Lee]

Hi Aishwarya,

Thank you for your question about how to use the reciprocal best chains file.

Questions about how to process data fall outside the scope of this mailing list,
thus how you choose to use the rbest file is up to you.

We recommend Biostars: https://www.biostars.org/
to get help with more general questions like this one.

Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply to gen...@soe.ucsc.edu. All messages
sent to that address are archived on a publicly-accessible forum. If your
question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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[aishwarya kulkarni]

Thanks Brian

I used following command to find the orthologs between humans and rats using rn6 rbest chains:

liftOver hg19_coordinates hg19.rn6.rbest.chain.gz  rat_coordinates unmapped_file

Is that the right approach to use?

Aishwarya.S.Kulkarni

[Christopher Lee]

Hi Aishwarya,

Thank you for your question about the correct command to find orthologs between
rat and humans. Your command is indeed correct. If you ever have questions about
what a Kent utility does, run the command with no arguments, like so:

$ liftOver

This will print a usage message explaining what the program does and its various
arguments and options.

Note that liftOver was designed to work between two different assemblies of the same
species, not across species, as in this case. Thus, although your command may
technically work, it may produce undesired results.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any
further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that
address are archived on a publicly-accessible forum. If your question includes sensitive
data, you may send it instead to genom...@soe.ucsc.edu.

[aishwarya kulkarni]

Thanks Chris, is there a substitute for liftOver that I can use from the available utilities in this case? Also is there a way to verify orthologs in genome browser?

Thanks

Aishwarya.S.Kulkarni

[Matthew Speir]

Hello Aishwarya,

Thank you for your question.

We do not have any utilities or tools specifically designed for identifying and verifying orthologs. As my colleague Chris stated, the liftOver command you proposed should work, and will likely give you results, but we can't really guarantee that the results will be exactly what you are looking for. You will need to verify the results yourself, and you will have to determine how to best verify them.

I would recommend doing some research on techniques other scientists have used to identify and verify orthologs between two organisms. I would search our mailing list archives to see what questions others have asked about orthologs and what recommendations they had for finding them: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/orthologs. And, I would ask your questions about identifying orthologs on the BioStars (https://www.biostars.org/) or SeqAnswers (http://seqanswers.com/) forums. Both of those forums are intended to help people with more general research questions and may be able to provide some advice on your experimental design.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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