Minimotif Library Analysis Software (8/3/11)

 Summary

We are building a library of minimotifs (concatamers of 100s of unique units into lengths of 1-100) and need to know the composition of motif in each clone and population statistics.  We have identified 4 common workflows which would be of interest.

 Inputs

+ DNA sequence files (S1-Sx). (text files with clone id and string of DNA letters.)  
+ SQL database of Minimotifs (table of motifs (M1 - Mx and sequences to be searched, and labels)  
+ Linker sequence for all motifs  
+ Restriction site sequence  

 Data Processing workflows

+ Single clone analysis
Read sequence file Si and report the following:
+ Identify motifs (M1 - Mx) present in DNA and their order
+ Confirm initiator motif and terminator motif and positions
+ Confirm proper insertion into two restriction sites.
+ Flag any incorrect assemblies and sequences with N positions
+ Report total number of minimotifs in clone
+ Generate a graph of overall structure, show linker regions that glue motifs together and alignment of motifs to sequences with labels.
+ Report any 1 nucleotide mutations in DNA  

 Read sequence files and report the following:

* Identify common motifs present in all clones (not initiator and terminator)
* Identify unique motifs present in each individual clone
* Counts of occurrences of above
* Identification of an clustering patterns of multiple motifs 
* Flag if there are any duplicate clones
* Flag if there is more than one initiator and terminator
* Flag clones with just and initiator and terminator

 Library coverage Read files and report
* Read file of motif names or ids
* Report statistics on each motif in the clones (occurrences, range of occurrences in clones, missing motifs in the library)

 96 well plate analysis
* Same as single clone analysis but reads an array of 96 ids from A to H and 1 through 12
* Also include plate
* Files will be named plate id_letter_number