N and X represent any letter and remain unchanged. With -e, this will trace the upper envelope. This allows pat- tern recognition across an indel of at most just under five patterns in length. Translate the nucleotide sequence in seqfile into a protein sequence. Sequences are truncated to be a multiple of three nucleotides in length.
Subsequent lines contain the sequence to be used.
Also, profile programs use alpha and beta to compute gap penalties only for the sequence being searched, not for the profile. The first line of a profile file contains its name. Indel substrings are penalized by a score of alpha for the first letter, and by beta for subsequent letters in the indel. The examples below illustrate the application of scoring parameters to evaluate alignments. In the examples below, localS is used.