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Missed affiliation of M.Roytberg: National Research University Higher School of Economics. (Mikhail Roytberg, 14 March 2013)

By author's mistake the affiliation of Mikhail A.Roytberg was not shown properly. The correct affiliation is as follows:
Mikhail A. Roytberg 2,3
2) Institute of Mathematical Problems in Biology, RAS, Pushchino, 142290, Russia
3) National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow, 101000, Russia read full comment

Comment on: Polyanovsky et al. Algorithms for Molecular Biology, 6:25

linear search results (Andrew Dalke, 25 May 2010)

The linear search implementation uses several layers of overhead on top of the CDK Tanimoto calculation code, which in turn creates an intermediate bitset object. I expect that quite a bit of the compute time is spent just in function call and object management overhead.

The linear search data structure uses a lot of memory. Based on figure 9, the implementation uses about 330 bytes for a 1024-bit fingerprint, which only needs 128 bytes. Adding perhaps 10 bytes for the identifier and a few bytes for overhead leads to a memory requirement of about 150 bytes, which is less than half used by the implementation.

I have implemented the linear search code using Python for file I/O and memory management and C for search speed. By using a single byte array, with the... read full comment

Comment on: Kristensen et al. Algorithms for Molecular Biology, 5:9

CHSMiner included in the Softpedia Mac OS software database (Zhen Wang, 25 May 2010)

CHSMiner has been added to Softpedia's database of software programs for Mac OS on May, 2010. It is featured with a description text, screenshots, download links and technical details on this page:
http://mac.softpedia.com/get/Math-Scientific/CHSMiner.shtml

CHSMiner has been tested in the Softpedia labs using several industry-leading security solutions and found to be completely clean of adware/spyware components. More information about the product's certification is available on this page:
http://mac.softpedia.com/progClean/CHSMiner-Clean-77916.html
read full comment

Comment on: Wang et al. Algorithms for Molecular Biology, 4:2

Phyloscan Version 2 web server is available. (Lee Newberg, 24 March 2009)

Carmack et al. (Algorithms for Molecular Biology 2007, doi:10.1186/1748-7188-2-1) includes a web link to the Phyloscan Version 1 web server, which analyzes genomic sequence data from E. coli and related proteobacteria. There is now a Phyloscan Version 2 web server that permits analysis of user-supplied sequence data. The new web server can be found at http://bayesweb.wadsworth.org/cgi-bin/phyloscanV2.pl. read full comment

Comment on: Carmack et al. Algorithms for Molecular Biology, 2:1

Benchmarking datasets available for download (Rodrigo Gouveia-Oliveira, 10 February 2009)

The datasets used for benchmarking in this paper are now available for download at:http://www.cbs.dtu.dk/services/InterMap3D/Coevolution_Benchmarking_datasets.zipWe hope they can be of use to other researchers. read full comment

Comment on: Gouveia-Oliveira et al. Algorithms for Molecular Biology, 2:12

Systems Biology? (Herbert Sauro, 05 July 2006)

I was interested to read about the new journal, Algorithms for Molecular Biology. I was curious to know whether the journal would accept algorithms related to systems biology? read full comment

Comment on: Morgenstern et al. Algorithms for Molecular Biology, 1:1