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Minimotif Library Analysis Software (8/3/11)

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BioClojure MiniApp 1 : DNASeqMiner

REQUIREMENTS :

This application takes, as input, two files

1) A motif file (A list of maps, with each map having a "motif=" key). [call each row a DnaMotif]
2) A DNA sequence file, which is FASTA formatted. [call each row a DnaSeq]

The program will

1) Provide a user interface to upload or paste inputs
2) Internalize and validate inputs (DnaSeq file and DnaMotif file)
3) Compare each DnaSeq to each DnaMotif (that is, look for the DnaMotif.motif attribute in the DnaSeq), store matches.
4) Present the results of (3) to the user in a single CSV file, of format

   motif, FASTA header, FASTA sequence

SPECIFICATIONS :



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 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
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