S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

R. A. Baeza-yates and C. H. Perleberg, Fast and practical approximate string matching, Information Processing Letters, vol.59, issue.1, pp.21-27, 1996.
DOI : 10.1016/0020-0190(96)00083-X
URL : ftp://sunsite.dcc.uchile.cl/pub/users/rbaeza/papers/approxsearchIPL96.ps.gz

C. Barton, C. Liu, and S. P. Pissis, On-Line Pattern Matching on Uncertain Sequences and Applications, In: COCOA. LNCS, vol.95, issue.3, pp.547-562, 2016.
DOI : 10.1016/j.ygeno.2009.12.003

P. Bille, G. M. Landau, R. Raman, K. Sadakane, S. R. Satti et al., Random Access to Grammar-Compressed Strings, pp.373-389, 2011.
DOI : 10.1137/1.9781611973082.30

T. Gagie, P. Gawrychowski, and S. J. Puglisi, Faster Approximate Pattern Matching in Compressed Repetitive Texts, pp.653-662, 2011.
DOI : 10.1109/TIT.1977.1055714
URL : http://www.cs.hut.fi/~travis/papers/isaac11.pdf

T. Gagie and S. J. Puglisi, Searching and indexing genomic databases via kernelization, Frontiers in Bioengineering and Biotechnology, vol.3, p.12, 2015.
DOI : 10.3389/fbioe.2015.00012
URL : https://doi.org/10.3389/fbioe.2015.00012

R. Grossi, C. S. Iliopoulos, C. Liu, N. Pisanti, S. P. Pissis et al., On-Line Pattern Matching on Similar Texts, Schloss Dagstuhl?Leibniz-Zentrum fuer Informatik, pp.1-914, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01526650

D. Gusfield, Algorithms on strings, trees, and sequences, 1997.
DOI : 10.1017/CBO9780511574931

J. Holub, W. F. Smyth, and S. Wang, Fast pattern-matching on indeterminate strings, Journal of Discrete Algorithms, vol.6, issue.1, pp.37-50, 2008.
DOI : 10.1016/j.jda.2006.10.003
URL : https://doi.org/10.1016/j.jda.2006.10.003

L. Huang, V. Popic, and S. Batzoglou, Short read alignment with populations of genomes, Bioinformatics, vol.29, issue.13, pp.361-370, 2013.
DOI : 10.1093/bioinformatics/btt215

C. S. Iliopoulos, R. Kundu, and S. P. Pissis, Efficient pattern matching in elasticdegenerate texts, LATA. LNCS, pp.131-142, 2017.
DOI : 10.1007/978-3-319-53733-7_9

T. Kociumaka, S. P. Pissis, and J. Radoszewski, Pattern Matching and Consensus Problems on Weighted Sequences and Profiles, pp.1-46, 2016.

G. Landau and U. Vishkin, Introducing efficient parallelism into approximate string matching and a new serial algorithm, Proceedings of the eighteenth annual ACM symposium on Theory of computing , STOC '86, pp.220-230, 1986.
DOI : 10.1145/12130.12152

S. Maciuca, C. Del-ojo-elias, G. Mcvean, and Z. Iqbal, A natural encoding of genetic variation in a Burrows-Wheeler transform to enable mapping and genome inference, WABI. LNCS, pp.222-233, 2016.

J. C. Na, H. Kim, H. Park, T. Lecroq, M. Léonard et al., FM-index of alignment: A compressed index for similar strings, Theoretical Computer Science, vol.638, pp.159-170, 2016.
DOI : 10.1016/j.tcs.2015.08.008

G. Navarro, Indexing Highly Repetitive Collections, IWOCA. LNCS, pp.274-279, 2012.
DOI : 10.1007/978-3-642-35926-2_29
URL : http://www.dcc.uchile.cl/%7Egnavarro/ps/iwoca12.pdf

R. Rahn, D. Weese, and K. Reinert, Journaled string tree--a scalable data structure for analyzing thousands of similar genomes on your laptop, Bioinformatics, vol.30, issue.24, pp.3499-3505, 2014.
DOI : 10.1093/bioinformatics/btu438

J. Sirén, Indexing Variation Graphs, 2017 Proceedings of the Ninteenth Workshop on Algorithm Engineering and Experiments (ALENEX), pp.13-27, 2017.
DOI : 10.1137/1.9781611974768.2

S. Wandelt and U. Leser, String searching in referentially compressed genomes, pp.95-102, 2012.