proteins date

[h.mogh...@znu.ac.ir]

Dear UCSC,

Thanks for your helpful site.

For my research, I need  proteins data for human all together, not each protein individually. How can I find this data?

Regards,

  Hanieh Moghaddasi

  Ph.D Student of Physics

  Department of Physics, University of Zanjan

  E-mail: h.mogh...@znu.ac.ir

[Chris Villarreal]

Dear Hanieh Moghaddasi,

Thank you for your question about the UCSC Genome Browser. If I understand your question correctly, you would like to download all protein sequences for the human genome. You can do this using the Table Browser. Navigate to the Table Browser by following the link:https://genome.ucsc.edu/cgi-bin/hgTables.

Then follow these steps:

1) Select the genome and assembly that you are interested in.

2) Select Genes and Gene Prediction tracks as the group

3) Then select the track that you are interested in: 
e.g. Known Genes, RefSeq Genes. There are several Gene Prediction tracks 
e.g. Geneid, Genscan, Ensembl Genes.

4) Select genome as the region.

5) Select sequence for the output format, then click "get output". On the following page, select protein then click "submit".

The output will be a FASTA file of protein sequences for the track that 
you chose.

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 V
UCSC Genome Browser

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[h.mogh...@znu.ac.ir]

Dear Chris,

Thanks a lot for your help.

It works for many species but for some species such as "Lancelet" of clade "Deuterostome  " after selecting the appropriate choices and clicking "get output", there is only one choice which is "genomic" while for many other species the choice"protein" also appears that is the desired output for me. Does it mean for these species the protein sequence is not available?

Kind Regards,

  Hanieh Moghaddasi

  Ph.D Student of Physics

  Department of Physics, University of Zanjan

  E-mail: h.mogh...@znu.ac.ir

[Chris Villarreal]

Dear Hanieh Moghaddasi,

Some of our assemblies such as the Lancelet are minimally annotated and don't display all of the same output options as more richly annotated assemblies. However, there is a way to display "Translated Protein from predicted mRNA" which provides the amino acid sequence for a particular gene region predicted by Augustus. To display "Translated Protein from predicted mRNA" follow these steps:

1. Set the Augustus track in the Lancelet browser to full.
2. Click on the gene to access the gene description page.
3. Under the heading "Links to sequence" choose the "Translated Protein from predicted mRNA" option.

Additionally, you can translate CDS nucleotide sequence from the Table Browser to protein sequence with the faTrans command line utility found here:http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. Follow these steps:
1. Click "the utilities directory" link.
2. Choose your operating system.
3. Download the faTrans utility.
4. View the usage statement for the desired output by typing in the command name without any arguments/options.

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 V
UCSC Genome Browser