ABI Chroma Align
(Polymorfic ABI Sequence Alignment) by Ivano Zara
Release 2011_04 (Beta Release)

With this application it is possible to align one or more ABI chromatogram sequences (Sanger method) (max 4) against a reference sequence.
The alignment of chromatograms and sequences (text format) facilitates their comparison. The program displays and highlights any inconsistencies.

The program is useful, in particular, if you sequence a particular gene (whose reference sequence is known) to verify the existence of possible mutations both in homozygosity and in heterozygosis.

The graphic display of the chromatograms, aligned to the reference sequence, facilitates the interpretation of any uncertainties of the bases of the sequences. In fact, sometimes background noise is interpreted automatically by the chromatograms as heterozygous polymorphisms. The alignment of the chromatograms with the possibility of zooming into a particular region, allows, for example, to visually verify the goodness of the prediction of particular mutations.
Overview * IT * * EN *

File ABI
togliere work_grup
Automatic translation (click for help)
REFERENCE SEQUENCE (one or more sequences in FASTA format)

Advance Setting

Minimum Ratio Secondary Base Signal on a Main Base:
A polymorphism will be signaled only if the signal ratio of the weakest (secondary) basewith the signal of the strongest (primary) base it is higher than this value
With low values, more polymorphisms are obtained, but these can be the effect of possible background noises

Sensitivity in alignment: Low
Depending on the choice, the Blast parameters will be set so that, with high sensitivity, the alignments will also extend to regions of low similarity. With medium sensitivity, default parameters will be adopted, while with low sensitivity only high similarity regions will be preferred

(**) Quality Sequence Setting
1° quality filters: Internal window
Internal Size (w)      Average Quality Threshold (q)
2° quality filters: External window for trimming
External Size (e)     Trimming quality threshold (t)
default parameters: w=21, q=20, e=5, t=10
(**)Quality Sequence Setting It is used to establish the high quality region of the ABI sequence. Low quality regions, which do not align with the reference, will be trimmed
There are 2 quality filters that can be applied either together or separately.
- The internal filter selects a region where the quality of a window (Internal Size) is always above an average quality (Average Quality Threshold).Setting 'Internal Size = 0' will turn off the internal filter.
- The 2nd filter applies to the ends: it scans each end with a window (External Size ) until it finds that all the bases are >= to the threshold quality (Trimming quality threshold ). Again, if 'External Size is 0' is given, the external filter is turned off.
Remember that the internal filter works on the average value, while the external works on the absence of values below 'Trimming quality threshold '.
If both filter are applied, then the internal filter will be applied first, then the external filter will check and trim the resulting ends.

First release 01_2011 created in January 2011
Second release 03_2011: The Phred program has been replaced with another self-made (used to determine any polymorphisms).
Third release 04_2011 direct link from the 'Chromatogram' program and modification of the entry form