November 2009 - galaxy-user - lists.galaxyproject.org

Getting sequences for multiple species from UCSC
by Farhat Habib 11 Nov '09

11 Nov '09

Hi all, I am wondering if there is a way to download sequence information from UCSC into Galaxy for multiple species. E.g, looking at a region of the genome for Drosophila melanogaster, you can also see the level of conservation across other insect species. Is it possible to get the sequences from all species that align to that region of the genome in Drosophila. Thanks. -Farhat

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Search for TF binding site patterns in Galaxy
by Brown, Stuart 05 Nov '09

05 Nov '09

I am trying to come up with a nice workflow/tutorial for the use of Galaxy to search for Transcription Factor binding sites on a genome wide scale using pattern search tools. I want to train my students to think genomically and to use clever tools to leverage their abilities. Galaxy is absolutely awesome for grabbing the upstream promoter regions for all genes from any organism with a whole genome in UCSC. It is also possible to use the integrated EMBOSS tools such as fuzznuc and dreg to search for a known TFBS (or any other simple nucleotide pattern). However, I can't get past the simple search into a more clever infomation-based search. In particular I have the following workflow in mind: 1. Collect upstream regions for all mouse (or human) genes 2. Search for a published TF binding site with a single base mismatch using FUZZNUC 3. Make a multiple alignment of the sequences returned by FUZZNUC (not possible in any way that I have been able to find) 4. Make a logo from the alignment to identify informative positions and conserved substitutions (not in Galaxy) 5. Make a PSSM profile, HMM profile, or other smart searching tool from the aligned sequences (not in Galaxy) 6. Search the upstream regions again with this more sensitive pattern search method. (not in Galaxy). 7. Make a list of genes targeted with this TFBS, 8. Compare list of genes to microarray data showing co-regulation of this gene set, or to pathways I am frustrated at step 3. Even if I bring the FUZZNUC results to my desktop, there is no easy way to extract just sequences and make a multiple alignment. Many of the 'allowed' Fuzznuc optional output formats produce an error, or no useable output. Thanks for any suggestions. Stuart M. Brown, Ph.D. Associate Professor Center for Health Informatics and Bioinformatics NYU School of Medicine 550 First Ave, NY, NY 10016 stuart.brown(a)med.nyu.edu (212)263-7689 FAX (212) 263-8139 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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Using mysql instead of sqlite
by Erick Antezana 04 Nov '09

04 Nov '09

Hello, I would like to use MySQL instead of sqlite to store my data. I coudn't find on the Galaxy web site a HOWTO or some guidelines to do it. I only found some lines that might need to be changed/enabled in the universe_wsgi.ini file: #database_file = database/universe.sqlite database_connection = mysql:///galaxy #database_engine_option_echo = true #database_engine_option_echo_pool = true #database_engine_option_pool_size = 10 #database_engine_option_max_overflow = 20 Could you point out to some doc or briefly describe what I need to do in order to go for mysql? Are there any plans to support other DBMS's (like Oracle for instance)? thanks, Erick

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Default global variables in Galaxy
by gerrit 04 Nov '09

04 Nov '09

Hi there, Can anyone tell where I can find a description of the default global variables in Galaxy. From the tool examples I can gather that GALAXY_DATA_INDEX_DIR is one but can not find documentation of any other. Thanks, Gerrit

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Experience with Loading NGS data on standalone instance of galaxy
by Abhishek Pratap 04 Nov '09

04 Nov '09

Hi All I recently came to know about NGS analysis on galaxy during ISMB. Getting excited I tried couple of things basically to play with it. Few comments : I may have interepretted something described below in a wrong way. My apologies before hand. On a standalone installation of galaxy while I was trying to explore one FASTQ(sequence) file. It takes considerable (> 20 min) for a fastq file to get uploaded (2 GB). I am not sure what is the rationale behind that. Ideally I think there should be no need to upload such heavy files into the workspace. They could actually be used straight away by the path specified. Also is there any way to access the scripts for analysis on the command line. I know this undermines the main aim of working with galaxy but rite now I am concerned about the performance/time. I will be happy to discuss more about this in case you have some comments/questions for me. Best, -Abhi ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/

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