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wrpearson / fasta36

Git repository for FASTA36 sequence comparison software
Apache License 2.0
117 stars 17 forks source link

Sliding window searches #16

Closed susheelbhanu closed 4 years ago

susheelbhanu commented 5 years ago

Dear Bill,

Firstly, thank you for the very nice tool. The following website http://www.allergenonline.org/databasefasta.shtml, seems to be using it with what is called a "80-mer sliding window" approach.

Is this something that can be implemented via your tool? I noticed that you have a "-v" option for window shuffling, but I presume this is not the same as the former.

Thank you, Susheel

wrpearson commented 4 years ago

The programs in the FASTA package are designed to do various kinds of local or global alignments. Sliding windows are not part of FASTA (the -v option sets a shuffle window length, for producing random sequences for statistical analysis).