PrimerDigital

Select one or more tools for simultaneous analysis: Tm, CG%, GA%, Linguistic Complexity, CG-AT skew, CG skew, AT skew, RY skew and Primer Quality; and use additional editor for selecting widow length (10 to 100,000) and press F5.
Primer Quality Plot is maximum 50 bases and 10 minimum bases widow length.
Output result as .XLS Text file, compatible for Excel or Open Office.

Random DNA Generation

Using additional editor, you can select the length for generation random DNA sequence with “Generate Random DNA”. Random DNA is useful for a design artificial primer, DNA adaptors.

Type the length of desire sequence at any Tabs:

Alignment Search

This tool can help to find sequence(s) with local alignment.
FastPCR allows the searching of related DNA sequence(s) within personal databases (in a similar way as in BLAST analysis). This is also convenient for primers selection and monitoring.


Moreover, as a basis for sequence alignment, the following idea was adopted: related sequences should have sequential common homologous blocks and inversions, deletions or permutations which are looked as gaps in sequence comparisons.
Alignment algorithm started for searching of exact word (9 as default) sequence which then extended to left and to right as not complete complement segment with no gap and scoring the strings similarity. The extension is done by pairwise character comparisons. The algorithm is direct compute maximal exact segment-substrings for many candidates. Finally, segment-substrings joined to long string with gaps. For increasing detection highly degenerated substrings FastPCR allows applying the purine-pyrimidine local alignment.
In aligning the DNA sequences the program uses the similarity table for all degenerated nucleotide that increases the probability of identifying related sequences.

Repeats Search

Repeats searching tool can perform quick search of all kinds of repeats. This fast and effective DNA analysis algorithm was developed for the search of composite and long repeats by alignment in the following formats; direct vs. direct, direct vs. reverse, direct vs. complement, direct vs. reverse-complement. Searching in all orientations facilitates the rapid identification of unique sequence representing long terminal repeats (LTR), tandem repeats, and even new retrotransposons (such as LARD or TRIM) and transposons (such as MITEs).

K-mers repeats screening

– is quickest way for discovering any king of repeats, without dot plot. Similar repeats are clustered and located at the same row (Y) and coordinates (X) for nucleotide position. All different repeats are stretching on Y coordinates:

This picture is BAC clone, contains several LTR retrotransposons, first two short LTRs (TRIM element) located between 42799- and 49932+ (show with black arrow and red ovals), and then followed 3 similar long length LTRs (57065, 71331 and 85596); same solo average LTRs (99862, 128394-135527):



The blue dots are shown the direct orientation repeats; red dots for opposite orientation for current type of repeat.
Initial searching work size, K=7 or 10, nt – quick (or instance) method for identification repeats based on defining high-frequency k-mer (short substrings of length k) as seeds, and greedily extends each seed to a progressively longer sequence, following it clustering for consensus sequence alignment. Software is capable of detecting degenerate substrings or repeats. Value “7” is 7 bases is used, and 10 bases for value 10. Value 10 allowed much quickest analysis, but at least 1 Gb free RAM memory is necessary.

To find all degenerate repeats (or substrings) user is specified alignment parameters: initial kmer size, minimum extended substring length with minimum similarity, maximum gap size and minimum repeat length.



Fig. 2 Show that 26.5% from 30.4M bases sequence of Arabidopsis thaliana chromosome 1 covering by repeats sequences. The centromere of chromosome 1 is easy to detect in the middle of picture by special structure of the clusters of centromeric repeats, also shown the chromosome duplications.