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AlignOneAll

Function AlignOneAll


Calling Sequence  AlignOneAll(seq,db,day,cutoff,entries)
Parameters
NameTypeDescription
seq {posint,string}a sequence or an entry number
db databasea DNA or protein database
day DayMatrixscoring matrix
cutoff numericonly matches with score > cutoff will be reported
entries posint..posint(optional) compare these entries in db only
Return Type  list(Match)
Synopsis Align seq against all members of the database db (or the subset of entries specified by the entries parameter when present) and return the list of matches which have a similarity score, using day, which exceeds cutoff. This function will return only one alignment per database sequence. If seq is a positive integer, then it is understood to be the sequence in that entry number. The alignments reported are Local alignments, that is the best subsequences are matched.

This type of search is similar to what FASTA and BLAST (Basic Local Alignment Search Tool) do. The main difference between them and AlignOneAll is that AlignOneAll does not use approximations, it does rigorous dynamic programming against all the sequences in the database. Its speed is comparable to the other programs, so we see no reason to use shortcuts when the exact results are easy to obtain.

Examples 
> DB := ReadDb('/home/darwin/DB/SwissProt.Z'):;

Peptide file(/home/darwin/DB/SP45.0/SwissProt45.0(169638448), 163235
 entries, 59631787 aminoacids)

> AlignOneAll('NKRSPAASQPPVSRVNPQEESYQKLAMETLEELDWCLD',DB,DM,110);

[Match(168.3,9748355,71916164,38,38,250),
 Match(147.5,9749450,71916164,38,38,250),
 Match(122.2,9752627,71916164,38,38,250),
 Match(122.2,9754188,71916164,38,38,250)]
See also DB,   SearchFrag,   SearchSeqDb