obtaining pairwise alignments from the table browser

[Eliot Bush]

hello,

I'd like to get human mouse pairwise alignments over some regions of
human chromosome 1. And have been trying to figure out if I can do
that with the table browser.

I can see there are various multiz tracks which include both mouse and
human. Is there some way that I can extract human and mouse alone from
those?

This is teaching related, so I'm especially looking for ways I can do
it online, ie without students having to download intermediate files
and process them locally. Ultimately we want something in fasta
format. (In the past I did something like this with Galaxy, but the
tools I used there no longer seem to be working).

thanks,
Eliot

[Gerardo Perez]

Hello, Eliot.

Thank you for your interest in the UCSC Genome Browser and for your question about obtaining pairwise alignments from the Table Browser.

To get human-to-mouse pairwise alignments, you can use the "CDS FASTA alignment from multiple alignment" output option in the Table Browser. You can do the following to get human-to-mouse pairwise alignments using the NCBI RefSeq track on the Table Browser:

1. Navigate to the Table Browser: Go to the Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables) and select the following options:

• Clade: Mammal
• Genome: Human
• Assembly: Dec. 2013 (GRCh38/hg38)
• Group: Genes and Gene Predictions
• Track: NCBI RefSeq
• Table: RefSeq All (ncbiRefSeq)

2. Define your regions: Click on "Define regions", paste your chromosome 1 regions or upload a file with your regions, and then click Submit.

3. Select output format: Choose "CDS FASTA alignment from multiple alignment" and click "Get output".

4. Specify the alignment options: On the “Select multiple alignment and options for NCBI RefSeq” page, choose a MAF table and any desired formatting options.

5. Select the mouse species: Click the [-] button to clear all species selections, select mouse, and click "Get output".

This will output the human-to-mouse pairwise alignments for your selected chromosome 1 regions.

I hope this is helpful. If you have any additional questions or need further assistance, 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.

Gerardo Perez
UCSC Genomics Institute

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