Hi Ben, I'll answer your questions in order: 1. Yes the Personal Genome SNP format would probably work best for your purposes.
2. We have documentation downloading and installing the browser. See: - http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads - http://genome.ucsc.edu/admin/jk-install.html - http://genomewiki.ucsc.edu/index.php/Category:Mirror_Site_FAQ The source code (see first link above) download also includes files with extensive install documentation in the kent/src/product/ directory. And there is information on our Wiki about adding your own custom reference sequence (i.e. assembly) to the browser: http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database If you do build your own mirror, you might also want to consider using a multiple-sequence aligner like multiz (or maybe some other tool for protein seqs) that produces MAF, since we have a very nice display built around that. See: http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto 3. There is currently no way to make AA the reference. 4. Unfortunately, I don't have any specifics on which browser is better for a given purpose. I would suggest asking those at NCBI specific questions you might have about their browser in order to make the best choice for the work you want to do. If you have any additional questions, please feel free to contact us again at: [email protected]. - Greg Roe UCSC Genome Bioinformatics Group On 4/4/11 6:30 AM, Ben Bimber wrote: > Hello, > > I have performed a lot of next gen sequencing, but am very new to the > genome browser and the associated file formats. I am trying to > understand what exists in this area and have a few basic questions. > > I am interested in writing tools to display SNP and other feature data > as custom tracks in some genome browser. Some of these features will > have insertions relative to the reference. I would like to use custom > non-human reference sequences (viral genomes). If possible, in some > contexts I'd also like to use an AA sequence as the reference, which > is distinct from displaying a NT reference with the translations > displayed. Most of my information about supported file formats has > come from this page: > > http://genome.ucsc.edu/FAQ/FAQformat.html > > Here are the questions: > > 1. Based on the above page, it seems that Personal Genome SNP format > is the best and possible only option to display indels relative to the > reference. Is this true? If not, how are short insertions (1-12nt) > usually represented? > > 2. I have been able to find very little in terms of creating custom > reference sequences using UCSC genome browser. I am assuming that if > i did a local install, this would be possible. Are there resources on > this topic I did not find? Can anyone comment on the process of > adding custom reference sequences? > > 3. Are there any capabilities to use an AA sequence as the reference. > It appears that a translation track can be shown; however, that's not > quite the same as a purely AA alignment. There's already a lot to > digest, and the simpler I can make the view the better. > > 4. I am also considering NCBI's sequence viewer for this project: > http://www.ncbi.nlm.nih.gov/projects/sviewer/ > > The advantages I see with the NCBI viewer are that it will support > many references, and can show AA alignments. Does anyone have > experience with this and do you have comments comparing it to the UCSC > genome browser? > > Thanks in advance for any help. I tried to research these in advance, > and apologize if I missed some obvious resources that answered these. > > -Ben Bimber > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
