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fastBlockSearch

By Stanke M., Keller O., Morgenstern B., Last update 1494698999
All tools Run in Terminal

fastBlockSearch description

FastBlockSearch performs preliminary search If a protein profile and a genome are given. It will output the locations of profile hits. An AUGUSTUS-PPX run can then be restricted to regions containing these locations. It should be run with the same parameters as the AUGUSTUS-PPX run. In addition, a threshold can be specified with the parameter --cutoff that controls the number of profile hits shown.


Parent program: augustus

AUGUSTUS is a software to predict genes in eukaryotic genomic sequences.The approach is based on a generalized Hidden Markov Model. AUGUSTUS parses a genomic sequence to segments that are most likely according to the underlying statistical models. The program is often the most accurate for ab initio gene prediction for the species it is trained for. AUGUSTUS is able to incorporate EST, mRNA and protein alignments. It also can predict alternative transcripts, splicing and 5'UTR and 3'UTR including introns with probabilities for the transcripts and each exon and intron.