question about the meaning of block in track Pfam in UCSC Gene

[wangcy]

Hi UCSC Group,

How are you! I am writing to ask what block definitely mean in track Pfam in UCSC Gene. Attached please find a snap of the description of that table. thank you!

Best,

Chengyang

[Chris Villarreal]

Hi Chengyang,

Thank you for your question about the UCSC Genome Browser.
Unfortunately we are having trouble viewing the photo you sent, are you referring to the ucscGenePfam table? If so, here is a link to the table schema:
https://genome.ucsc.edu//cgi-bin/hgTables?db=hg38&hgta_group=genes&hgta_track=ucscGenePfam&hgta_table=ucscGenePfam&hgta_doSchema=describe+table+schema

The blockCounts and blockSizes refer to the number and size of each block you see when you look at the track in the browser. 

If this is not the table you are referring to please let us know!

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.

Chris Villarreal
UCSC Genome Bioinformatics Group

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[wangcy]

Hi Chris,

Thank you for your reply, This is what I care about. I want to know the biological meaning of each “block” in Pfam.

Below is an example.

"

586	chr1	187278	195374	WASH_WAHD	0	-	0	0	0	10	9,202,132,7,4,141,48,96,112,116,	0,97,476,743,823,847,1160,1210,1512,7980,

“

In which there are 10 blocks for domain WASH_WAHD locating from 187278 to 195374. What does block mean in here? It means exons or segmentation of protein domain or any others? thank you!

Best,

Chengyang

[Jairo Navarro Gonzalez]

Hello Chengyang,

Thank you for your question about the UCSC Genome Browser.

The blocks indicate regions in the genome that are likely to code for the particular Pfam-A domain. For example, in the WASH_WAHD case, you can count the 10 blocks notated in the below session:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=jnavarr5&hgS_otherUserSessionName=WASH_WAHD

Together these 10 blocks annotate the genomic sequence that will become the WASH_WAHD domain after translation.

For more information about the Pfam Domains in UCSC Genes track, see the track description page:
http://genome.ucsc.edu/cgi-bin/hgc?db=hg38&c=chr1&l=187278&r=195374&o=187278&t=195374&g=ucscGenePfam&i=WASH_WAHD

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.

Jairo Navarro
UCSC Genome Bioinformatics Group

[wangcy]

Hi Chris,

Thank you very much for your clarification. I never thought Pfam domain could be noncontiguous within it! 

Best,

Chengyang