     funnel.doc                                          update 10/27/90

                             FUNNEL                          
     I. Function- Reads in a DNA or RNA sequence and writes it to a file, 
        with a fixed number or characters (LINELENGTH) per line, as set by 
        user.

     NOTE: FUNNEL WILL NOT WORK CORRECTLY ON BIONET OR GENBANK FILES.

     NEW FEATURES
     The right arrow (>) is also interpreted by FUNNEL as a comment.
     This is convenient for FUNNELing Pearson format files.
   
     The maximum line length is set to 10000, to permit the generation of
     long output lines, that are sometimes convenient to have.
     
     DESCRIPTION
     The most efficient way to type in a sequence is by spacing every five or 
     ten bases.  This makes proofreading easy.  However, blank spaces make a 
     file bigger than it needs to be, and therefore slower for a program to 
     read.  FUNNEL's job is to take a sequence, after it has been stored as a 
     TEXT file and proofread, and compress it into a file containing a 
     user-specified number of bases on each line (LINESIZE). FUNNEL 
     faithfully copies upper and lower case letters (amino acid sequences as 
     well as nucleic acids), from one file to another.  Comments are also 
     transferred, although each comment in the reformatted file will be 
     written to a separate line. FUNNEL is most useful when used in 
     conjunction with NUMSEQ.  If a sequence has previously been numbered 
     with NUMSEQ, one can write changes (such as insertions or deletions 
     based on new sequencing experiments) on the NUMSEQ printout, and then go 
     back to the original file, formatted by FUNNEL, and easily find the 
     corresponding region, using the numbered printout as a guide. 

     Parameters:
     LINESIZE     no. of nucleotides written per line to output file.

     Example:
     Given the following input file,
     ; EXP #190
     gggca cccaa ttata ccctt cccta ggtagttta ntttc tttcc cagagc ccaga ccatt
     tttca cccc tatgg cagat ccatg gacca tcaat tatat ttaca
     cctt aaaaa aacaa atata
     ; EXP #191 & #192
     gatac cataa aacct TTAAT AAAAA AAAAC CAATA CATTA CAAAT
     TATAT aACCAG GAAGA GAATT

     and specifying LINESIZE to be 40,FUNNEL will produce the output file

     ; EXP #190
     gggcacccaattatacccttccctaggtagtttantttct
     ttcccagagcccagaccatttttcacccctatggcagatc
     catggaccatcaattatatttacaccttaaaaaaacaaat
     ata
     ; EXP #191 & #192
     gataccataaaacctTTAATAAAAAAAAACCAATACATTA
     CAAATTATATaACCAGGAAGAGAATT
