icamatches - print concise multiple alignments


     icamatches  [-index  filename ] [-ini  filename ]


     ICAmatches takes an index file produced by any ICAtool clus-
     tering program and prints a series of sequence alignments to
     the screen(stdout).  This index file includes references  to
     necessary  other  files  containing  the DNA sequences.  All
     these files must be exactly as they were when the index  was

     ICAmatches multiple DNA sequence alignments  are  much  more
     concise  than  the usual style of multiple alignment because
     they only show the (complete length of) a single type  exam-
     ple  sequence.   Underneath this type sequence is listed the
     number of similar sequences that match  to  that  particular
     region.   The totals of matching sequence segments are aver-
     aged over 5-base windows.   The  type  example  sequence  is
     chosen  by the program used to produce the submitted cluster
     index and not by ICAmatches itself.  The alignments are pro-
     duced  one for each cluster and printed in the same order as
     found in the cluster index file.  If no sequences were found
     to be similar, then no alignments will be produced.  Regard-
     less  of  the  algorithm  used  to  cluster  the   sequences
     together,  ICAmatches  will  only aim to discover and record
     the presence of a single best matching, un-gapped  alignment
     between the type sequence and others in the same cluster.

     ICAmatches ability to display both the frequency and map the
     position of any common sequence motifs makes it an extremely
     useful tool when searching for  sequencing  artefacts.   For
     various  reasons,  ICAmatches  works  best with the clusters
     produced by N2tool but useful information can be  discovered
     by using ICAmatches with any type of cluster index.


  -index filename
     Defines  the  name   of   the   index   file.   Default   is
     "cluster.index" in the current directory.

  -ini filename
     Defines the name of the file which holds the user's  initial
     configuration  file. Default is "ICAtool.ini" in the current


     If this file  is  present  or  another  ini  file  has  been
     defined,  then  all startup details present in the file will
     be read. An example showing only relevant lines would be:

     This  cluster  index  file,  or  its  replacement,  must  be


     N2tool(1), ICAtool(1), ICAass(1), ICAprint(1),  ICAstats(1),
     ssort(1), tofasta(1), just30(1)