#Snapgene find orf software#

Specifying a negative n implies -n*patternLength

join|-j = Join anchors within n bases of eachother (default: 0) hashCache|-c = Caches hash tables in the directory. Not supplying any argument increments the skip amount by 1. skip1to1|-1 = Skip matches along the 1:1 line (good for comparing to self) skiprev|-R = Skip reverse facing matches skipfwd|-F = Skip forward facing matches Use the same seed for each run of the same settings.ĭefault is obtained from time() ( ie: seconds since 1970). Performance comparisons, it's probably imperative that you rseed|-s = random number seed for non-deterministic algorithms So more like at best 1/N the tolerance of seedfilter. May cause some collateral damage to otherwise hashfilter|-m= like -seedfilter but works on hash keys instead of seedfilter|-f= skip seeds that occur more than N times repeatmask|-r= skip repeat masked data ( ie: lowercase atgc) histogram|-H = histogram computation level: (-H alone implies -H1)ġ - basic bucketsize/bucketcount histogram dataĢ - bucket-based scores to tils hitfilter|-h = minimum number of hits to be outputted as an anchor probing = 0 - linear, 1 - quadratic (default) MSetHash - memory exorbanant, almost pointless. OpenHash - open sub-word packing of hashbitsĮcoHash - chained sub-word packing of hashbits (default)ĪrrayHash - malloc/realloc (fast but fragmenty) hashtype|-t = select hash table data structure to use: hashbits|-b = use n bit hashes (for n's of 1 to WORDSIZE. quickhash|-q = specify a hashing function:ġ - don't pack bits to make hash (use first word only)Ģ - naively use the first hashbits worth of patternģ - adaptivevely find a good hash (default)

name|-n = alignment name (default: test) directory|-d = output directory (default: output) Using the format automatically generates a $ docker run -rm -it biocontainers/murasaki:v1.68.6-8b1- deb_cv1 murasaki -h > docker run -rm -it biocontainers/murasaki:v1.68.6-8b1- deb_cv1 murasaki -h

MUMmer4: A fast and versatile genome alignment system Stefan Kurtz*, Adam Phillippy†, Arthur L Delcher†, Michael Smoot†‡, Martin Shumway†, Corina Antonescu† and Steven L Salzberg†

#Snapgene find orf software#

３、 Versatile and open software for comparing large genomes

２、 Fast algorithms for large-scale genome alignment and comparison.ĭelcher AL1, Phillippy A, Carlton J, Salzberg SL. SnapGene software (from GSL Biotech available at ) SnapGene Viewer | Molecular Biology Software SnapGene Software Tutorial Videos | Aligning to a Reference DNA Sequence SnapGene | Software for everyday molecular biology