LAF: Logic Alignment Free and its application to bacterial genomes classification
Identifieur interne : 000E14 ( Pmc/Checkpoint ); précédent : 000E13; suivant : 000E15LAF: Logic Alignment Free and its application to bacterial genomes classification
Auteurs : Emanuel Weitschek [Italie] ; Fabio Cunial [Finlande] ; Giovanni Felici [Italie]Source :
- BioData Mining [ 1756-0381 ] ; 2015.
Abstract
Alignment-free algorithms can be used to estimate the similarity of biological sequences and hence are often applied to the phylogenetic reconstruction of genomes. Most of these algorithms rely on comparing the frequency of all the distinct substrings of fixed length (
In this paper, we present Logic Alignment Free (
We apply
State of the art methods to adjust the frequency of
Url:
DOI: 10.1186/s13040-015-0073-1
PubMed: 26664519
PubMed Central: 4673791
Affiliations:
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PMC:4673791Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">LAF: Logic Alignment Free and its application to bacterial genomes classification</title>
<author><name sortKey="Weitschek, Emanuel" sort="Weitschek, Emanuel" uniqKey="Weitschek E" first="Emanuel" last="Weitschek">Emanuel Weitschek</name>
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<author><name sortKey="Felici, Giovanni" sort="Felici, Giovanni" uniqKey="Felici G" first="Giovanni" last="Felici">Giovanni Felici</name>
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<series><title level="j">BioData Mining</title>
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<front><div type="abstract" xml:lang="en"><p>Alignment-free algorithms can be used to estimate the similarity of biological sequences and hence are often applied to the phylogenetic reconstruction of genomes. Most of these algorithms rely on comparing the frequency of all the distinct substrings of fixed length (<italic>k</italic>
-mers) that occur in the analyzed sequences.</p>
<p>In this paper, we present Logic Alignment Free (<sc>LAF</sc>
), a method that combines alignment-free techniques and rule-based classification algorithms in order to assign biological samples to their taxa. This method searches for a minimal subset of <italic>k</italic>
-mers whose relative frequencies are used to build classification models as disjunctive-normal-form logic formulas (<italic>if-then rules</italic>
).</p>
<p>We apply <sc>LAF</sc>
successfully to the classification of bacterial genomes to their corresponding taxonomy. In particular, we succeed in obtaining reliable classification at different taxonomic levels by extracting a handful of rules, each one based on the frequency of just few <italic>k</italic>
-mers.</p>
<p>State of the art methods to adjust the frequency of <italic>k</italic>
-mers to the character distribution of the underlying genomes have negligible impact on classification performance, suggesting that the signal of each class is strong and that <sc>LAF</sc>
is effective in identifying it.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pearson, Wr" uniqKey="Pearson W">WR Pearson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Needleman, Sb" uniqKey="Needleman S">SB Needleman</name>
</author>
<author><name sortKey="Wunsch, Cd" uniqKey="Wunsch C">CD Wunsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pearson, Wr" uniqKey="Pearson W">WR Pearson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name>
</author>
<author><name sortKey="Madden, Tl" uniqKey="Madden T">TL Madden</name>
</author>
<author><name sortKey="Schaffer, Aa" uniqKey="Schaffer A">AA Schaffer</name>
</author>
<author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name>
</author>
<author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name>
</author>
<author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edgar, Rc" uniqKey="Edgar R">RC Edgar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Thompson, Jd" uniqKey="Thompson J">JD Thompson</name>
</author>
<author><name sortKey="Gibson, T" uniqKey="Gibson T">T Gibson</name>
</author>
<author><name sortKey="Higgins, Dg" uniqKey="Higgins D">DG Higgins</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mokaddem, A" uniqKey="Mokaddem A">A Mokaddem</name>
</author>
<author><name sortKey="Elloumi, M" uniqKey="Elloumi M">M Elloumi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Katoh, K" uniqKey="Katoh K">K Katoh</name>
</author>
<author><name sortKey="Misawa, K" uniqKey="Misawa K">K Misawa</name>
</author>
<author><name sortKey="Kuma, K I" uniqKey="Kuma K">K-i Kuma</name>
</author>
<author><name sortKey="Miyata, T" uniqKey="Miyata T">T Miyata</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vinga, S" uniqKey="Vinga S">S Vinga</name>
</author>
<author><name sortKey="Almeida, J" uniqKey="Almeida J">J Almeida</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Kasif, S" uniqKey="Kasif S">S Kasif</name>
</author>
<author><name sortKey="Fleischmann, Rd" uniqKey="Fleischmann R">RD Fleischmann</name>
</author>
<author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name>
</author>
<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, M" uniqKey="Li M">M Li</name>
</author>
<author><name sortKey="Vitnyi, Pmb" uniqKey="Vitnyi P">PMB Vitnyi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Almeida, Js" uniqKey="Almeida J">JS Almeida</name>
</author>
<author><name sortKey="Vinga, S" uniqKey="Vinga S">S Vinga</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vinga, S" uniqKey="Vinga S">S Vinga</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vinga, S" uniqKey="Vinga S">S Vinga</name>
</author>
<author><name sortKey="Almeida, J" uniqKey="Almeida J">J Almeida</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bentley, Sd" uniqKey="Bentley S">SD Bentley</name>
</author>
<author><name sortKey="Parkhill, J" uniqKey="Parkhill J">J Parkhill</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Josse, J" uniqKey="Josse J">J Josse</name>
</author>
<author><name sortKey="Kaiser, A" uniqKey="Kaiser A">A Kaiser</name>
</author>
<author><name sortKey="Kornberg, A" uniqKey="Kornberg A">A Kornberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Trautner, T" uniqKey="Trautner T">T Trautner</name>
</author>
<author><name sortKey="Swartz, M" uniqKey="Swartz M">M Swartz</name>
</author>
<author><name sortKey="Kornberg, A" uniqKey="Kornberg A">A Kornberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Russell, G" uniqKey="Russell G">G Russell</name>
</author>
<author><name sortKey="Walker, P" uniqKey="Walker P">P Walker</name>
</author>
<author><name sortKey="Elton, R" uniqKey="Elton R">R Elton</name>
</author>
<author><name sortKey="Subak Sharpe, J" uniqKey="Subak Sharpe J">J Subak-Sharpe</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Russell, G" uniqKey="Russell G">G Russell</name>
</author>
<author><name sortKey="Subak Sharpe, J" uniqKey="Subak Sharpe J">J Subak-Sharpe</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name>
</author>
<author><name sortKey="Burge, C" uniqKey="Burge C">C Burge</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name>
</author>
<author><name sortKey="Mrazek, J" uniqKey="Mrazek J">J Mrázek</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Teeling, H" uniqKey="Teeling H">H Teeling</name>
</author>
<author><name sortKey="Meyerdierks, A" uniqKey="Meyerdierks A">A Meyerdierks</name>
</author>
<author><name sortKey="Bauer, M" uniqKey="Bauer M">M Bauer</name>
</author>
<author><name sortKey="Amann, R" uniqKey="Amann R">R Amann</name>
</author>
<author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glöckner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhou, F" uniqKey="Zhou F">F Zhou</name>
</author>
<author><name sortKey="Olman, V" uniqKey="Olman V">V Olman</name>
</author>
<author><name sortKey="Xu, Y" uniqKey="Xu Y">Y Xu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Deschavanne, Pj" uniqKey="Deschavanne P">PJ Deschavanne</name>
</author>
<author><name sortKey="Giron, A" uniqKey="Giron A">A Giron</name>
</author>
<author><name sortKey="Vilain, J" uniqKey="Vilain J">J Vilain</name>
</author>
<author><name sortKey="Fagot, G" uniqKey="Fagot G">G Fagot</name>
</author>
<author><name sortKey="Fertil, B" uniqKey="Fertil B">B Fertil</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sandberg, R" uniqKey="Sandberg R">R Sandberg</name>
</author>
<author><name sortKey="Winberg, G" uniqKey="Winberg G">G Winberg</name>
</author>
<author><name sortKey="Br Nden, Ci" uniqKey="Br Nden C">CI Bränden</name>
</author>
<author><name sortKey="Kaske, A" uniqKey="Kaske A">A Kaske</name>
</author>
<author><name sortKey="Ernberg, I" uniqKey="Ernberg I">I Ernberg</name>
</author>
<author><name sortKey="Coster, J" uniqKey="Coster J">J Cöster</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pride, Dt" uniqKey="Pride D">DT Pride</name>
</author>
<author><name sortKey="Meinersmann, Rj" uniqKey="Meinersmann R">RJ Meinersmann</name>
</author>
<author><name sortKey="Wassenaar, Tm" uniqKey="Wassenaar T">TM Wassenaar</name>
</author>
<author><name sortKey="Blaser, Mj" uniqKey="Blaser M">MJ Blaser</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gatherer, D" uniqKey="Gatherer D">D Gatherer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Takahashi, M" uniqKey="Takahashi M">M Takahashi</name>
</author>
<author><name sortKey="Kryukov, K" uniqKey="Kryukov K">K Kryukov</name>
</author>
<author><name sortKey="Saitou, N" uniqKey="Saitou N">N Saitou</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Teeling, H" uniqKey="Teeling H">H Teeling</name>
</author>
<author><name sortKey="Waldmann, J" uniqKey="Waldmann J">J Waldmann</name>
</author>
<author><name sortKey="Lombardot, T" uniqKey="Lombardot T">T Lombardot</name>
</author>
<author><name sortKey="Bauer, M" uniqKey="Bauer M">M Bauer</name>
</author>
<author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glockner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rigoutsos, I" uniqKey="Rigoutsos I">I Rigoutsos</name>
</author>
<author><name sortKey="Floratos, A" uniqKey="Floratos A">A Floratos</name>
</author>
<author><name sortKey="Ouzounis, C" uniqKey="Ouzounis C">C Ouzounis</name>
</author>
<author><name sortKey="Gao, Y" uniqKey="Gao Y">Y Gao</name>
</author>
<author><name sortKey="Parida, L" uniqKey="Parida L">L Parida</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chor, B" uniqKey="Chor B">B Chor</name>
</author>
<author><name sortKey="Horn, D" uniqKey="Horn D">D Horn</name>
</author>
<author><name sortKey="Goldman, N" uniqKey="Goldman N">N Goldman</name>
</author>
<author><name sortKey="Levy, Y" uniqKey="Levy Y">Y Levy</name>
</author>
<author><name sortKey="Massingham, T" uniqKey="Massingham T">T Massingham</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="O Ul, H" uniqKey="O Ul H">H Oğul</name>
</author>
<author><name sortKey="Mumcuo Lu, Eu" uniqKey="Mumcuo Lu E">EÜ Mumcuoğlu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name>
</author>
<author><name sortKey="Mrazek, J" uniqKey="Mrazek J">J Mrazek</name>
</author>
<author><name sortKey="Campbell, Am" uniqKey="Campbell A">AM Campbell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Foerstner, Ku" uniqKey="Foerstner K">KU Foerstner</name>
</author>
<author><name sortKey="Von Mering, C" uniqKey="Von Mering C">C von Mering</name>
</author>
<author><name sortKey="Hooper, Sd" uniqKey="Hooper S">SD Hooper</name>
</author>
<author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mchardy, Ac" uniqKey="Mchardy A">AC McHardy</name>
</author>
<author><name sortKey="Martin, Hg" uniqKey="Martin H">HG Martín</name>
</author>
<author><name sortKey="Tsirigos, A" uniqKey="Tsirigos A">A Tsirigos</name>
</author>
<author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name>
</author>
<author><name sortKey="Rigoutsos, I" uniqKey="Rigoutsos I">I Rigoutsos</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chatterji, S" uniqKey="Chatterji S">S Chatterji</name>
</author>
<author><name sortKey="Yamazaki, I" uniqKey="Yamazaki I">I Yamazaki</name>
</author>
<author><name sortKey="Bai, Z" uniqKey="Bai Z">Z Bai</name>
</author>
<author><name sortKey="Eisen, Ja" uniqKey="Eisen J">JA Eisen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Leung, Hc" uniqKey="Leung H">HC Leung</name>
</author>
<author><name sortKey="Yiu, S" uniqKey="Yiu S">S Yiu</name>
</author>
<author><name sortKey="Yang, B" uniqKey="Yang B">B Yang</name>
</author>
<author><name sortKey="Peng, Y" uniqKey="Peng Y">Y Peng</name>
</author>
<author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name>
</author>
<author><name sortKey="Liu, Z" uniqKey="Liu Z">Z Liu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name>
</author>
<author><name sortKey="Leung, Hc" uniqKey="Leung H">HC Leung</name>
</author>
<author><name sortKey="Yiu, S" uniqKey="Yiu S">S Yiu</name>
</author>
<author><name sortKey="Chin, Fy" uniqKey="Chin F">FY Chin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tanaseichuk, O" uniqKey="Tanaseichuk O">O Tanaseichuk</name>
</author>
<author><name sortKey="Borneman, J" uniqKey="Borneman J">J Borneman</name>
</author>
<author><name sortKey="Jiang, T" uniqKey="Jiang T">T Jiang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Song, K" uniqKey="Song K">K Song</name>
</author>
<author><name sortKey="Ren, J" uniqKey="Ren J">J Ren</name>
</author>
<author><name sortKey="Zhai, Z" uniqKey="Zhai Z">Z Zhai</name>
</author>
<author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name>
</author>
<author><name sortKey="Deng, M" uniqKey="Deng M">M Deng</name>
</author>
<author><name sortKey="Sun, F" uniqKey="Sun F">F Sun</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stuart, Gw" uniqKey="Stuart G">GW Stuart</name>
</author>
<author><name sortKey="Moffett, K" uniqKey="Moffett K">K Moffett</name>
</author>
<author><name sortKey="Baker, S" uniqKey="Baker S">S Baker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stuart, Gw" uniqKey="Stuart G">GW Stuart</name>
</author>
<author><name sortKey="Moffett, K" uniqKey="Moffett K">K Moffett</name>
</author>
<author><name sortKey="Leader, Jj" uniqKey="Leader J">JJ Leader</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
<author><name sortKey="Verzotto, D" uniqKey="Verzotto D">D Verzotto</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kuksa, P" uniqKey="Kuksa P">P Kuksa</name>
</author>
<author><name sortKey="Pavlovic, V" uniqKey="Pavlovic V">V Pavlovic</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Solovyev, Vv" uniqKey="Solovyev V">VV Solovyev</name>
</author>
<author><name sortKey="Makarova, Ks" uniqKey="Makarova K">KS Makarova</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ratnasingham, S" uniqKey="Ratnasingham S">S Ratnasingham</name>
</author>
<author><name sortKey="Hebert, Pdn" uniqKey="Hebert P">PDN Hebert</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name>
</author>
<author><name sortKey="Gibbons, T" uniqKey="Gibbons T">T Gibbons</name>
</author>
<author><name sortKey="Ghodsi, M" uniqKey="Ghodsi M">M Ghodsi</name>
</author>
<author><name sortKey="Treangen, T" uniqKey="Treangen T">T Treangen</name>
</author>
<author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Segata, N" uniqKey="Segata N">N Segata</name>
</author>
<author><name sortKey="Waldron, L" uniqKey="Waldron L">L Waldron</name>
</author>
<author><name sortKey="Ballarini, A" uniqKey="Ballarini A">A Ballarini</name>
</author>
<author><name sortKey="Narasimhan, V" uniqKey="Narasimhan V">V Narasimhan</name>
</author>
<author><name sortKey="Jousson, O" uniqKey="Jousson O">O Jousson</name>
</author>
<author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C Huttenhower</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edwards, Ra" uniqKey="Edwards R">RA Edwards</name>
</author>
<author><name sortKey="Olson, R" uniqKey="Olson R">R Olson</name>
</author>
<author><name sortKey="Disz, T" uniqKey="Disz T">T Disz</name>
</author>
<author><name sortKey="Pusch, Gd" uniqKey="Pusch G">GD Pusch</name>
</author>
<author><name sortKey="Vonstein, V" uniqKey="Vonstein V">V Vonstein</name>
</author>
<author><name sortKey="Stevens, R" uniqKey="Stevens R">R Stevens</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Seth, S" uniqKey="Seth S">S Seth</name>
</author>
<author><name sortKey="V Lim Ki, N" uniqKey="V Lim Ki N">N Välimäki</name>
</author>
<author><name sortKey="Kaski, S" uniqKey="Kaski S">S Kaski</name>
</author>
<author><name sortKey="Honkela, A" uniqKey="Honkela A">A Honkela</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weitschek, E" uniqKey="Weitschek E">E Weitschek</name>
</author>
<author><name sortKey="Fiscon, G" uniqKey="Fiscon G">G Fiscon</name>
</author>
<author><name sortKey="Felici, G" uniqKey="Felici G">G Felici</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lehr, T" uniqKey="Lehr T">T Lehr</name>
</author>
<author><name sortKey="Yuan, J" uniqKey="Yuan J">J Yuan</name>
</author>
<author><name sortKey="Zeumer, D" uniqKey="Zeumer D">D Zeumer</name>
</author>
<author><name sortKey="Jayadev, S" uniqKey="Jayadev S">S Jayadev</name>
</author>
<author><name sortKey="Ritchie, M" uniqKey="Ritchie M">M Ritchie</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Polychronopoulos, D" uniqKey="Polychronopoulos D">D Polychronopoulos</name>
</author>
<author><name sortKey="Weitschek, E" uniqKey="Weitschek E">E Weitschek</name>
</author>
<author><name sortKey="Dimitrieva, S" uniqKey="Dimitrieva S">S Dimitrieva</name>
</author>
<author><name sortKey="Bucher, P" uniqKey="Bucher P">P Bucher</name>
</author>
<author><name sortKey="Felici, G" uniqKey="Felici G">G Felici</name>
</author>
<author><name sortKey="Almirantis, Y" uniqKey="Almirantis Y">Y Almirantis</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kudenko, D" uniqKey="Kudenko D">D Kudenko</name>
</author>
<author><name sortKey="Hirsh, H" uniqKey="Hirsh H">H Hirsh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ben Hur, A" uniqKey="Ben Hur A">A Ben-Hur</name>
</author>
<author><name sortKey="Brutlag, D" uniqKey="Brutlag D">D Brutlag</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xing, Z" uniqKey="Xing Z">Z Xing</name>
</author>
<author><name sortKey="Pei, J" uniqKey="Pei J">J Pei</name>
</author>
<author><name sortKey="Keogh, E" uniqKey="Keogh E">E Keogh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kuksa, P" uniqKey="Kuksa P">P Kuksa</name>
</author>
<author><name sortKey="Pavlovic, V" uniqKey="Pavlovic V">V Pavlovic</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vapnik, Vn" uniqKey="Vapnik V">VN Vapnik</name>
</author>
<author><name sortKey="Vapnik, V" uniqKey="Vapnik V">V Vapnik</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bertolazzi, P" uniqKey="Bertolazzi P">P Bertolazzi</name>
</author>
<author><name sortKey="Felici, G" uniqKey="Felici G">G Felici</name>
</author>
<author><name sortKey="Weitschek, E" uniqKey="Weitschek E">E Weitschek</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weitschek, E" uniqKey="Weitschek E">E Weitschek</name>
</author>
<author><name sortKey="Lo Presti, A" uniqKey="Lo Presti A">A Lo Presti</name>
</author>
<author><name sortKey="Drovandi, G" uniqKey="Drovandi G">G Drovandi</name>
</author>
<author><name sortKey="Felici, G" uniqKey="Felici G">G Felici</name>
</author>
<author><name sortKey="Ciccozzi, M" uniqKey="Ciccozzi M">M Ciccozzi</name>
</author>
<author><name sortKey="Ciotti, M" uniqKey="Ciotti M">M Ciotti</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gaines, Br" uniqKey="Gaines B">BR Gaines</name>
</author>
<author><name sortKey="Compton, P" uniqKey="Compton P">P Compton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Frank, E" uniqKey="Frank E">E Frank</name>
</author>
<author><name sortKey="Witten, Ih" uniqKey="Witten I">IH Witten</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cohen, Ww" uniqKey="Cohen W">WW Cohen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Felici, G" uniqKey="Felici G">G Felici</name>
</author>
<author><name sortKey="Truemper, K" uniqKey="Truemper K">K Truemper</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bertolazzi, P" uniqKey="Bertolazzi P">P Bertolazzi</name>
</author>
<author><name sortKey="Felici, G" uniqKey="Felici G">G Felici</name>
</author>
<author><name sortKey="Weitschek, E" uniqKey="Weitschek E">E Weitschek</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Quinlan, Jr" uniqKey="Quinlan J">JR Quinlan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hall, M" uniqKey="Hall M">M Hall</name>
</author>
<author><name sortKey="Frank, E" uniqKey="Frank E">E Frank</name>
</author>
<author><name sortKey="Holmes, G" uniqKey="Holmes G">G Holmes</name>
</author>
<author><name sortKey="Pfahringer, B" uniqKey="Pfahringer B">B Pfahringer</name>
</author>
<author><name sortKey="Reutemann, P" uniqKey="Reutemann P">P Reutemann</name>
</author>
<author><name sortKey="Witten, Ih" uniqKey="Witten I">IH Witten</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marcais</name>
</author>
<author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Dasarathy, Bv" uniqKey="Dasarathy B">BV Dasarathy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Teeling, H" uniqKey="Teeling H">H Teeling</name>
</author>
<author><name sortKey="Meyerdiekers, A" uniqKey="Meyerdiekers A">A Meyerdiekers</name>
</author>
<author><name sortKey="Bauer, M" uniqKey="Bauer M">M Bauer</name>
</author>
<author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glockner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pride, Dt" uniqKey="Pride D">DT Pride</name>
</author>
<author><name sortKey="Meinersmann, Rj" uniqKey="Meinersmann R">RJ Meinersmann</name>
</author>
<author><name sortKey="Wassenaar, Tm" uniqKey="Wassenaar T">TM Wassenaar</name>
</author>
<author><name sortKey="Blaser, Mj" uniqKey="Blaser M">MJ Blaser</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Teeling, H" uniqKey="Teeling H">H Teeling</name>
</author>
<author><name sortKey="Waldmann, J" uniqKey="Waldmann J">J Waldmann</name>
</author>
<author><name sortKey="Lombardot, T" uniqKey="Lombardot T">T Lombardot</name>
</author>
<author><name sortKey="Bauer, M" uniqKey="Bauer M">M Bauer</name>
</author>
<author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glockner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chan, Rh" uniqKey="Chan R">RH Chan</name>
</author>
<author><name sortKey="Chan, Th" uniqKey="Chan T">TH Chan</name>
</author>
<author><name sortKey="Yeung, Hm" uniqKey="Yeung H">HM Yeung</name>
</author>
<author><name sortKey="Wang, Rw" uniqKey="Wang R">RW Wang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name>
</author>
<author><name sortKey="Wang, B" uniqKey="Wang B">B Wang</name>
</author>
<author><name sortKey="Hao, Bi" uniqKey="Hao B">BI Hao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yu, Zg" uniqKey="Yu Z">ZG Yu</name>
</author>
<author><name sortKey="Zhou, Lq" uniqKey="Zhou L">LQ Zhou</name>
</author>
<author><name sortKey="Anh, Vv" uniqKey="Anh V">VV Anh</name>
</author>
<author><name sortKey="Chu, Kh" uniqKey="Chu K">KH Chu</name>
</author>
<author><name sortKey="Long, Sc" uniqKey="Long S">SC Long</name>
</author>
<author><name sortKey="Deng, Jq" uniqKey="Deng J">JQ Deng</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Song, K" uniqKey="Song K">K Song</name>
</author>
<author><name sortKey="Ren, J" uniqKey="Ren J">J Ren</name>
</author>
<author><name sortKey="Reinert, G" uniqKey="Reinert G">G Reinert</name>
</author>
<author><name sortKey="Deng, M" uniqKey="Deng M">M Deng</name>
</author>
<author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name>
</author>
<author><name sortKey="Sun, F" uniqKey="Sun F">F Sun</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Huang, K" uniqKey="Huang K">K Huang</name>
</author>
<author><name sortKey="Brady, A" uniqKey="Brady A">A Brady</name>
</author>
<author><name sortKey="Mahurkar, A" uniqKey="Mahurkar A">A Mahurkar</name>
</author>
<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
<author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name>
</author>
<author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C Huttenhower</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BioData Min</journal-id>
<journal-id journal-id-type="iso-abbrev">BioData Min</journal-id>
<journal-title-group><journal-title>BioData Mining</journal-title>
</journal-title-group>
<issn pub-type="epub">1756-0381</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26664519</article-id>
<article-id pub-id-type="pmc">4673791</article-id>
<article-id pub-id-type="publisher-id">73</article-id>
<article-id pub-id-type="doi">10.1186/s13040-015-0073-1</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Methodology</subject>
</subj-group>
</article-categories>
<title-group><article-title>LAF: Logic Alignment Free and its application to bacterial genomes classification</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Weitschek</surname>
<given-names>Emanuel</given-names>
</name>
<address><email>emanuel@iasi.cnr.it</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
<xref ref-type="aff" rid="Aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cunial</surname>
<given-names>Fabio</given-names>
</name>
<address><email>cunial@cs.helsinki.fi</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Felici</surname>
<given-names>Giovanni</given-names>
</name>
<address><email>giovanni.felici@iasi.cnr.it</email>
</address>
<xref ref-type="aff" rid="Aff3">3</xref>
</contrib>
<aff id="Aff1"><label>1</label>
Department of Engineering, Uninettuno International University, Corso Vittorio Emanuele II, 39, Rome, 00186 Italy</aff>
<aff id="Aff2"><label>2</label>
Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, P.O. Box 68 (Gustaf Hällströmin katu 2b), Helsinki, FI-00014 Finland</aff>
<aff id="Aff3"><label>3</label>
Institute of Systems Analysis and Computer Science “A. Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy</aff>
</contrib-group>
<pub-date pub-type="epub"><day>8</day>
<month>12</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>8</day>
<month>12</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="collection"><year>2015</year>
</pub-date>
<volume>8</volume>
<elocation-id>39</elocation-id>
<history><date date-type="received"><day>30</day>
<month>3</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>30</day>
<month>11</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-statement>© Weitschek et al. 2015</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><p>Alignment-free algorithms can be used to estimate the similarity of biological sequences and hence are often applied to the phylogenetic reconstruction of genomes. Most of these algorithms rely on comparing the frequency of all the distinct substrings of fixed length (<italic>k</italic>
-mers) that occur in the analyzed sequences.</p>
<p>In this paper, we present Logic Alignment Free (<sc>LAF</sc>
), a method that combines alignment-free techniques and rule-based classification algorithms in order to assign biological samples to their taxa. This method searches for a minimal subset of <italic>k</italic>
-mers whose relative frequencies are used to build classification models as disjunctive-normal-form logic formulas (<italic>if-then rules</italic>
).</p>
<p>We apply <sc>LAF</sc>
successfully to the classification of bacterial genomes to their corresponding taxonomy. In particular, we succeed in obtaining reliable classification at different taxonomic levels by extracting a handful of rules, each one based on the frequency of just few <italic>k</italic>
-mers.</p>
<p>State of the art methods to adjust the frequency of <italic>k</italic>
-mers to the character distribution of the underlying genomes have negligible impact on classification performance, suggesting that the signal of each class is strong and that <sc>LAF</sc>
is effective in identifying it.</p>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Supervised classification</kwd>
<kwd>Alignment-free sequence comparison</kwd>
<kwd>Bacterial taxonomy</kwd>
</kwd-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2015</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Finlande</li>
<li>Italie</li>
</country>
<region><li>Latium</li>
<li>Uusimaa</li>
</region>
<settlement><li>Helsinki</li>
<li>Rome</li>
</settlement>
<orgName><li>Université d'Helsinki</li>
</orgName>
</list>
<tree><country name="Italie"><region name="Latium"><name sortKey="Weitschek, Emanuel" sort="Weitschek, Emanuel" uniqKey="Weitschek E" first="Emanuel" last="Weitschek">Emanuel Weitschek</name>
</region>
<name sortKey="Felici, Giovanni" sort="Felici, Giovanni" uniqKey="Felici G" first="Giovanni" last="Felici">Giovanni Felici</name>
<name sortKey="Weitschek, Emanuel" sort="Weitschek, Emanuel" uniqKey="Weitschek E" first="Emanuel" last="Weitschek">Emanuel Weitschek</name>
</country>
<country name="Finlande"><region name="Uusimaa"><name sortKey="Cunial, Fabio" sort="Cunial, Fabio" uniqKey="Cunial F" first="Fabio" last="Cunial">Fabio Cunial</name>
</region>
</country>
</tree>
</affiliations>
</record>
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