USAGE : alignthingie.pl [options] blast.out 

  COMMAND-LINE OPTIONS:

    -c : Minimum number of conserved residues (or '+') allowed around the matche
d residue (integer, def : 6)
    -C : Also check for Cs in the subject sequence which align to a '*' in the query
    -e : Maximum e-value allowed (integer, def : 10)
    -i : Minimum (i)dentity percentage allowed (integer, def : 0)
    -I : Maximum (I)dentity percentage allowed (integer, def : 100)
    -l : Minimum number of conserved residues (or '+') allowed on the (l)eft side of the matched residue
         (def : 3)
    -r : Minimum number of conserved residues (or '+') allowed on the (r)ight side of the matched residue
         (def : 3)       
    -M : (M)aximum score value allowed (integer, def : 10000)
    -m : (m)inimum score value allowed (integer, def : 0)
    -q : String to match in query (def : '*' )
    -s : String to match in subject     (def : '*')
    -R : Length of (R)egion around matched residue to check for conservation (integer, def : 6)
         (R-matched residue-R)   
    -S : Use strict evalue, id, score (0.01,65,50 respectively) and conservation cuttoffs.
         Writing the cons cuttoffs too long, just run "alignthingie.pl -Sd" to see...
    -k : Do not check conservation
    -u : How many (u)naligned residues are allowed with respect to query length.  
         ( -  <= )

OUTPUT OPTIONS:
    -A :  Return (A)ll HSPs which pass thresholds without looking for any specific aligned residues
    -b :  Print only the (b)est (lowest e-value) hit for each query. If the smallest evalue
          is shared by more than one HSP, all such HSPs will be printed.
    -B :  Print only the (B)est (lowest e-value) hit for each query. If the smallest evalue
          is shared by more than one HSP, only the first such HSP will be printed.
    -d : (d)ebugging mode, very very verbose...
    -f :  No sel(f) : Skips subjects whose name matches (case-INsensitive) the value passed. (string)
    -F :  Generalised no sel(F), takes first chars (till first space, OR value passed) of query and subj names and 
          skips the hit if the 2 are identical.
    -g : (g)ff output. Use "-g q" for guery position gff and "-g s" for subject gff.
    -L :  Print most (L)ikely hits. ie, those with no stop codon before the matched residue and whose
          conservation on the right side of the match is no more than 2 less than that of the left side.
          (this option is really only useful for selenoprotein searches)
    -n :  Print only the names of those queries which did NOT return any HSP.
    -p :  Do not return hits against (p)lant species.
    -Q : (Q)uery name or list of names (text file, one name per line) to return HSPs for. Only those HSPs whose 
          query is specified will be printed
    -T : (T)arget (subject) name or list of names (text file, one name per line) to return HSPs for. 
          Only those HSPs whose subject is specified will be printed
    -v : (v)erbose output, prints a . for each query processed.
    -V :  more (V)erbose output, prints a . for each query processed and a ! for each hit found.
    -x : Only return those hits with a redox box CXXU/*
    -X : Read a list of species names and ignore hits between the same species.
    -U : Query name or list of (U)nwanted queries. Quoted list of query names (or text file, one name per line)
         for which NOT to return HSPs.

  USAGE: retrieveseqs.pl [-viofsn] <FASTA sequence file> <desired IDs, one per line>
  
  COMMAND-LINE OPTIONS:
    -v : verbose output, print a progress indicator (a "." for every 1000 sequences processed)
    -V : as above but a "!" for every desired sequence found.
    -f : fast, takes first characters of name "(/^([^\s]*)/)" given until the first space as the search string
         make SURE that those chars are UNIQUE.
    -i : use when the ids in the id file are EXACTLY identical
         to those in the FASTA file
    -h : Show this help and exit.
    -o : will create one fasta file for each of the id files
    -s : will create one fasta file per id
    -n : means that the last arguments (after the sequence file)
         passed are a QUOTED list of the names desired.

  USAGE  : SECISearch [OPTIONS] -p [patscan pattern file] [FASTA input file]
    
  COMMAND-LINE OPTIONS:
    -c : Patscan will search the complimentary strand
    -d : Debugging mode (very very very verbose)
    -e : Free energy cut-off value of the entire structure
    -t : Return <FILENAME>.<PATNAME>.hits
    -g : Create <FILENAME>.<PATNAME>.gff
    -G : Create gff in geneid format (score=1), use with -g or -o gff.
    -h : Display this message and exit
    -H : Produce HTML output
    -I : Do not return images
    -l : Print structures which did not pass the thermodynamic evaluation to the logfile.
    -o : Choice of STDOUT output format, can be 'fs' for fasta 
         or 'gff' for GFF. The default output is fasta. 
    -n : Return <FILENAME>.en
    -p : Pattern file passed to scan_for_matches. If '-p' is not given, the standard 
         pattern is used. Possible values are 's' for a standard pattern, 'n' for a 
         non-standard pattern, and 't' for a "twilight zone" pattern. Any bareword 
         value is assumed to be one of the patterns stored in the ~/share/SECISearch
         directory (or wherever else the patterns happen to be stored on your system).
         Any directory address will be assumed to be the location of a user defined 
         pattern file. CAUTION: SECISearch will not warn you if you give a non-existant
         filename as a pattern, so check your pattern name before running.
    -P : Do not run patscan. (input file must be in the format of patscan's output) 
    -R : Do not run RNAfold
    -s : Do NOT return <FILENAME>.<PATNAME>.secis, FASTA file of SECIS elements
    -T : Print total number of SECIS found
    -v : Verbose output
    -x : Create the log file "secislog"

SECIS Structural Feature Options (ON by default, use these options to turn the filters OFF):
    
    -B : Discards SECISes with at least 2 more unpaired nts on the 5'
         side than on the 3' side (visually bended to the left)
    -O : Discards SECISes with more than 2 consecutive,
         unpaired nts on any strand in the first 7nt after the quartet
    -Y : Discards Y-shaped SECISes 
    -S : Discards structures with less than 8 pairs