Hi Scott, On 04/08/2013 11:04 AM, Scott Schwartz wrote: > Hi Herve -- You might not be who I need to ask about this, but, the > stringDist (biostrings) function computes a matrix of all pairwise > distances. Is there any way to have it just return the first row of > this matrix to save computation time? There is indeed room for improving the facilities for computing string distances in Biostrings. This won't happen in the next couple of weeks though... In the meantime, if you need the Hamming distance (i.e. nb of mismatches only, this implies that all your strings have the same length), you can use neditAt(): > neditAt("ACT", DNAStringSet(c("AAA", "ACT", "ATT"))) [,1] [,2] [,3] [1,] 2 0 1 The above corresponds to the first col of the matrix below: > stringDist(c("ACT", "AAA", "ACT", "ATT"), method="hamming") 1 2 3 2 2 3 0 2 4 1 2 1 If you need the Levenshtein distance, you could use the stringdist package from CRAN: > library(stringdist) > stringdist("ACT", c("AAA", "CT", "ACTT")) [1] 2 1 1 This corresponds to the first col of the matrix below: > stringDist(c("ACT", "AAA", "CT", "ACTT")) 1 2 3 2 2 3 1 3 4 1 3 2 Cheers, H. > > Thanks in advance, and apologies if this is an unwelcome request. > > Best, > Scott > > > Scott Schwartz, PhD > Statistical Geneticist and Bioinformatics Scientist, > Genomics and Bioinformatics > Texas AgriLife Research > Texas A&M System > Rm 175 - Norman E. Borlaug Center > College Station, TX 77843-2123 > > Email: sschwartz at ag.tamu.edu > Office: (979) 845-1068 > Cell: (210) 296-4392 > Website: http://www.txgen.tamu.edu > <https: agrilifepeople.tamu.edu="" index.cfm="" event="" publicdirectory="" whi="" chentity="" 3="" whichunit="" 425=""/> -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319