Manual

(Short version for the online analyses, check the download page for the full guide)

Basic parameters:

- Base to search [G]: Letter that is used to detect the islands. G is used by default but other letters can be selected and used for the analysis instead (case-sensitive, use UPPERCASE).

- Min island length [2]: This parameter defines the length for the islands (m). It is also possible to select a range of lengths by adding the parameter Max island length (M) to detect all the islands that are in the range of length [m..M]. While all the possible islands of the different lengths in the range are detected, only islands of the same length can be part of the same PQS. To allow for mismatched islands use the parameter Max number of mismatches [0] to set the maximum number of mismatched islands allowed.

- Max loop distance [12]: This parameter defines the maximum distance (loop distance) that is allowed between two consecutive islands within the same PQS.

- Number of bulges [0]: This parameter defines the maximum number of gaps that can be opened per island. Alternatively, or in combination, the parameter Length of bulges [0] defines the maximum cumulative length of the gaps that is permitted per island. Finally, the flag No core defines whether at least two consecutive bases are required to define an island. This Boolean flag allows to detect also islands that do not have a “core” of at least two consecutive bases (e.g. G, GtGaG).

- Number of consecutive islands [4]: This parameter defines the number of islands that are required to be consecutive in the same PQS.

- Min number of perfect islands [1]: This parameter defines the minimum number of islands that are required to be “perfect” within each PQS. Since the tool allows to detect also islands that are degenerate, this parameter imposes a constraint for the minimum number of islands that cannot contain any degeneration within each pattern. Use 0 to detect PQS with no minimum number of perfect islands.

- Max number of long loops [1]: This parameter defines the maximum number of long loops (>= 7 nt) that are allowed within each PQS.

Loop symmetry check:

- Mirror: Evaluates the symmetry of the long loops (>= 7 nt) to improve the score, MIRROR symmetry is considered. Allows to detect longer loops with mirror properties that can form Hoogsteen-hairpins.

- Palindrome: Evaluates the symmetry of the long loops (>= 7 nt) to improve the score, PALINDROMIC symmetry is considered. Allows to detect longer loops with palindromic properties that can form canonical-hairpins.

- Mixed: Evaluates the symmetry of the long loops (>= 7 nt) to improve the score, MIXED MIRROR-PALINDROMIC symmetry is considered. Allows to detect longer loops with mirror and palindromic properties that can form mixed-hairpins.

Output (TAB separated)

Each line contains the sequence ID as in the fasta input, the start and the end indexes, the length of the islands, the score and the sequence for the PQS. The values are separated by TAB. In the PQS sequence the islands are represented in CAPS LOCK and are connected to loops by '-': 'ISL-loop-ISL-loop-ISL-loop-...-ISL'. Null loops are represented as 'ISL--ISL'.

Output with alignments

When showing the alignment, in between each PQS (in tsv format) it is shown the optimal alignment for each of the loops. '|' represent a Watson-Crick pairing, ':' represent a Hoogsteen pairing.