Ten Conferences WORDS: Open Problems and Conjectures

In connection to the development of the field of Combinatorics on Words, we present a list of open problems and conjectures that were stated during the ten last meetings WORDS. We wish to continually update the present document by adding informations concerning advances in problems solving

Closed, Palindromic, Rich, Privileged, Trapezoidal, and Balanced Words in Automatic Sequences

We prove that the property of being closed (resp., palindromic, rich, privileged trapezoidal, balanced) is expressible in first-order logic for automatic (and some related) sequences. It therefore follows that the characteristic function of those n for which an automatic sequence x has a closed (resp., palindromic, privileged, rich, trape- zoidal, balanced) factor of length n is automatic. For privileged words this requires a new characterization of the privileged property. We compute the corresponding characteristic functions for various famous sequences, such as the Thue-Morse sequence, the Rudin-Shapiro sequence, the ordinary paperfolding sequence, the period-doubling sequence, and the Fibonacci sequence. Finally, we also show that the function counting the total number of palindromic factors in a prefix of length n of a k-automatic sequence is not k-synchronized

Unary patterns under permutations

Thue characterized completely the avoidability of unary patterns. Adding function variables gives a general setting capturing avoidance of powers, avoidance of patterns with palindromes, avoidance of powers under coding, and other questions of recent interest. Unary patterns with permutations have been previously analysed only for lengths up to 3. Consider a pattern $p=\pi_{i_1}(x)\ldots \pi_{i_r}(x)$, with $r\geq 4$, $x$ a word variable over an alphabet $\Sigma$ and $\pi_{i_j}$ function variables, to be replaced by morphic or antimorphic permutations of $\Sigma$. If $|\Sigma|\ge 3$, we show the existence of an infinite word avoiding all pattern instances having $|x|\geq 2$. If $|\Sigma|=3$ and all $\pi_{i_j}$ are powers of a single morphic or antimorphic $\pi$, the length restriction is removed. For the case when $\pi$ is morphic, the length dependency can be removed also for $|\Sigma|=4$, but not for $|\Sigma|=5$, as the pattern $x\pi^2(x)\pi^{56}(x)\pi^{33}(x)$ becomes unavoidable. Thus, in general, the restriction on $x$ cannot be removed, even for powers of morphic permutations. Moreover, we show that for every positive integer $n$ there exists $N$ and a pattern $\pi^{i_1}(x)\ldots \pi^{i_n}(x)$ which is unavoidable over all alphabets $\Sigma$ with at least $N$ letters and $\pi$ morphic or antimorphic permutation

A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

<p>Abstract</p> <p>Background</p> <p>It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete.</p> <p>Results</p> <p>In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments? (3) In case of conserved palindromes, is it always the case that the whole conserved pattern is also symmetrical? (4) Do palindromic protein sequences form regular secondary structures? (5) Does sequence similarity of the two "sides" of a palindrome imply structural similarity? For the first question, we showed that the complexity of palindromic peptides is significantly lower than randomly generated palindromes. Therefore, one can say that palindromes occur frequently in low complexity protein segments, without necessarily having a defined function or forming a special structure. Nevertheless, this does not rule out the possibility of finding palindromes which play some roles in protein structure and function. In fact, we found several palindromes that overlap with conserved protein Blocks of different functions. However, in many cases we failed to find any symmetry in the conserved regions of corresponding Blocks. Furthermore, to answer the last two questions, the structural characteristics of palindromes were studied. It is shown that palindromes may have a great propensity to form α-helical structures. Finally, we demonstrated that the two sides of a palindrome generally do not show significant structural similarities.</p> <p>Conclusion</p> <p>We suggest that the puzzling abundance of palindromic sequences in proteins is mainly due to their frequent concurrence with low-complexity protein regions, rather than a global role in the protein function. In addition, palindromic sequences show a relatively high tendency to form helices, which might play an important role in the evolution of proteins that contain palindromes. Moreover, reverse similarity in peptides does not necessarily imply significant structural similarity. This observation rules out the importance of palindromes for forming symmetrical structures. Although palindromes frequently overlap with conserved Blocks, we suggest that palindromes overlap with Blocks only by coincidence, rather than being involved with a certain structural fold or protein domain.</p