SeqMan v.2 - Manipulations with sequences

BestPal_empirical - Calculates best palindrome for given rna sequence, and also a set suboptimal palindromes (sorted by energy)

BestPal_helix - Calculates best palindrome for given rna sequence with restrictions

BestPal_window - Calculates best palindrome for given rna sequence scanning the sequence with a window (for long sequences)

SMAP - mapping oligonucleotides to genome

OLIGS - Compute statistics of oligonucleotide occurrences in a set of sequences

OLIGSR - Compute statistics of oligonucleotide redundant occurrences in a set of sequences

OLIGS2 - Compute more frequently oligonucleotides in 1 set and less frequently oligonucleotides in 2 set

The programs usage in Scientific publications

FoldRNA - RNA secondary structure prediction through energy minimization

BestPal1 (empirical) - Calculates best palindrome for given rna sequence, and also a set suboptimal palindromes (sorted by energy)

BestPal2_1 (helix) - Calculates best palindrome for given rna sequence with restrictions

BestPal2_2 (window) - Calculates best palindrome for given rna sequence scanning the sequence with a window (for long sequences)

FindTerm Finding Terminators in bacterial genomes

findMiRNA - programm for search MiRNA

TargetMiRna - search for microRNA (miRNA) sites in genomic sequences