Question On Megablast Databases

Question: Question On Megablast Databases

5.5 years ago by

Dear galaxy members, I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with - 1. htgs 28-Jan-2013 2. nt 28-Jan-2013 3. wgs 28-Jan-2013 4. phiX174 Is there any further information to guide which database would be appropriate to use? In addition, how to find the genome information contained in each database? Many thanks, Kathryn

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modified 5.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.5 years ago by Sun, Wenping [USA] • 230

5.5 years ago by

Jennifer Hillman Jackson ♦ 25k

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Jennifer Hillman Jackson ♦ 25k wrote:

Hi Kathryn, These first three are three different types of sequence databases available from GenBank The last is a genome assembly for the phiX174 genome. Information about all can be found here: http://www.ncbi.nlm.nih.gov/genbank/ There are many uses, one example is covered in our Metagenomics publication: https://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k

Jen, Thank you very much for the information. They are very informative. I found the htgs and wgs databases information there. What does nt 28-Jan-2013 stand for? Meantime, if I am looking for virus containing database, I found wgs is one. Can anyone confirm or advice further if there is other options (database)? Thank you again! Kathryn To: Sun, Wenping [USA] Cc: galaxy-user@lists.bx.psu.edu Subject: [External] Re: [galaxy-user] Question on megablast databases Hi Kathryn, These first three are three different types of sequence databases available from GenBank The last is a genome assembly for the phiX174 genome. Information about all can be found here: http://www.ncbi.nlm.nih.gov/genbank/ There are many uses, one example is covered in our Metagenomics publication: https://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter Thanks! Jen Galaxy team Dear galaxy members, I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with - 1. htgs 28-Jan-2013 2. nt 28-Jan-2013 3. wgs 28-Jan-2013 4. phiX174 Is there any further information to guide which database would be appropriate to use? In addition, how to find the genome information contained in each database? Many thanks, Kathryn ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD REPLY • link written 5.5 years ago by Sun, Wenping [USA] • 230

Hello, "nt" refers to the "nucleotide" database. It is also linked from the link below, to here: http://www.ncbi.nlm.nih.gov/nuccore The "Quick start guide" can answer many questions about it: http://www.ncbi.nlm.nih.gov/books/NBK44863/ A good technical content description is here: ftp://ftp.ncbi.nlm.nih.gov/blast/db/README For viral only, there is a genbank division "VRL", that could be used in a local or cloud install with megablast: http://www.ncbi.nlm.nih.gov/genbank/htgs/divisions/ There are other options, a quick search brings up many alternatives, but you can review these to see which are the best fit for your own project's goals. Best, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD REPLY • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k

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