New Post: Building MBF v2.0 Preview
You can unblock the zip file before extracting and then all extracted files become unblocked as well. Also extracting with WinRar should produce unblocked files since WinRar doesn't care about this...
View ArticleNew Post: MBF installer - wrong .dll reference
The V2 beta 1 MBF installer will install .CSproj files to your machine, however the references are set to the wrong .dll's. If you open the project from the beta you will be missing references.We are...
View ArticleNew Post: Where and how do you set match and mismatch score before doing...
I know we can set GapOpenCost or GapExtensionCost etc. to aligner, for example:Bio.Algorithms.MUMmer.MUMmerAligner myMummer = new Bio.Algorithms.MUMmer.MUMmerAligner (); SimilarityMatrix mySimMatrix =...
View ArticleNew Post: Where and how do you set match and mismatch score before doing...
Hi Chris, and thanks for your post.One of our developers have suggested the following, hope it helps:Match and Mismatch scores are properties of similarity matrices and not aligners. It is used only...
View ArticleNew Post: Setting Similarity Matrix in MBF
Greetings,I am using Bio library (MBF 2.0) for sequence alignment, and I have a general Question. While we can select various options for an aligner, such as Gap Open Cost, etc, including similarity...
View ArticleNew Post: Setting Similarity Matrix in MBF
Hi kponcodeplex2011One of our Developers gave me the below infromation: We have 11 well defined Similarity Matrices in Bio.dll. These matrices are constructed from the resource files (.txt). You can...
View ArticleNew Post: NUCmer parameters "--maxmatch" and "--nooptimize"
Hi,The NUCmer aligner in MBF uses different names for some of the MUMmer/NUCmer parameters. Why didn't you use the same parameter names in MBF as in NUCmer/MUMmer?In addition, some of these parameters...
View ArticleNew Post: NUCmer parameters "--maxmatch" and "--nooptimize"
Sending for Bob, who is on vacation: Hi Robert,You should be able to use the -maxmatch flag to nucmerutil.exe. (I think the short form is -x) You can look at the code in nucmerutil if you want to see...
View ArticleNew Post: Venn Diagram based on Genomic Intervals issue
Hello Everyone,I have results from two ChipSeq experiments. Experiment A has 1900 peaks and Experiment B has 4000 peaks.When I create Venn Diagram using the interval data, the total number of...
View ArticleNew Post: Venn Diagram based on Genomic Intervals issue
Hi Vivek,It has been a while since I looked at the interval or VennDiagram code, so I am not sure exactly what you are trying to do and the steps you are using to do it. It sounds like you want to...
View ArticleNew Post: Venn Diagram based on Genomic Intervals issue
Thank you for the reply.I am trying to do the following.I have two ChipSeq results. These consist of interval data, chromosome, start, end, peak location and peak height.I want to see the number of...
View ArticleNew Post: Another genome browser framework
I just listened the MBF introduction in vienna ISMB 2011 conference, and it's really beautiful. And I want to talk to you in face during poster session, but I did not find somebody in front of your...
View ArticleNew Post: Another genome browser framework
You attended the presentation done by Simon Mercer. His Microsoft email address is simon.mercer@microsoft.com. Feel free to include myself (Rick Benge) in the correspondence. I am the community program...
View ArticleNew Post: Another genome browser framework
Hello Wang,Thanks for your interest in MBF, I'm sorry I missed you at the poster. I would be very interested in learning more about your project, and if there is any way in which MBF can assist you. As...
View ArticleNew Post: Attendance at Hackathon 2011
I was just curious if anyone in the community might be attending Hackathon 2011 -http://2011.biohackathon.org/home.I would love to see an MBF entry but I haven't heard of anyone at this point and it...
View ArticleNew Post: use of HPC pack 2008 to launch Microsoft Assembler like a cluster...
hey everybody!!!! i'm using a cluster with microsoft technologys with 3 nodes, using windows server HPC 2008, with HPC pack 2008 , i need to run microsoft assembler, but its imposible, because i have...
View ArticleNew Post: use of HPC pack 2008 to launch Microsoft Assembler like a cluster...
Leonard, thanks for your post. Just to clarify you are trying to run the Sequence assembler GUI based sample app on a cluster. I guess the first thing to examine is your file location spelling....
View ArticleNew Post: use of HPC pack 2008 to launch Microsoft Assembler like a cluster...
Leonard and I have exchanged some emails and I wanted to recap for the community here.The Sequence Assembler application is provided as a demonstration application only – it shows what can be done...
View ArticleNew Post: A utility like UCSC liftover
Just wondering if MBF supply a liftover utility like the one provided by UCSC http://genome.ucsc.edu/cgi-bin/hgLiftOver
View ArticleNew Post: A utility like UCSC liftover
The LiftOver utility provided by UCSC converts genome annotations from one assembly to another. This requires a defined transform between the source and target assembly, or a route from source to...
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