dataesr/scientific-paragraphs-categorization huggingface dataset:
The sequences are available from the GenBank database under accession numbers KF261354-KF261553. The ITS data set was supplemented with 58 Paxillus sequences from GenBank, mainly generated by  Hedh et al. (2008)   and Vellinga et al. (2012) (Table 2). They include the ITS sequences of white variants (JN661721 and JN673368), the ITS sequence of Paxillus ammoniavirescens (IB1997_0980) and Paxillus obscurisporus (CH290_98) types, the ITS sequences of the genomesequenced strain ATCC 200175, and some sequences obtained from ectomycorrhizal tips. One tef and two gpd Paxillus sequences from GenBank were also included in the analyses ( Table  2 ). All our references to species from the literature refer to collections that are recognized by sequence data.
Phylogenetic and statistical analyses Sequence chromatograms were manually checked to identify heterozygous nucleotide position and sequences were manually corrected using BioEdit software (Hall 1999). Multiple sequence alignments were conducted for the three nuclear regions ITS rDNA, gpd, and tef in SeaView v4. 0  ( Galtier et al. 1996 ) using MUSCLE v3. 7 (Edgar 2004). The three alignments were concatenated into a single sequence alignment of 1686 bp. Alignments are available on treebase. org under the following link http://purl. org/phylo/treebase/phylows/study/TB2:S14414. The evolutionary model was selected by using jModelTest-2. 1. 4 (Darriba et al. 2012). Phylogenetic analyses were performed using the Bayesian inference with MrBayes v3. 2 (Ronquist et al. 2012) , with six Markov Chain Monte Carlo (MCMC) ran simultaneously for 2 000 000 generations (tef and gpd) or 3 000 000 generations (ITS, concatenated) under GTR + gamma evolutionary model.
Trees were saved every 500 generations and the first 25 % were discarded as 'burn-in'. For the remaining trees, a majority rule consensus tree was computed to obtain estimates for Bayesian posterior probabilities. Phylogenetic trees were visualized and edited with FigTree v1. 4. 0 available at http://tree. bio. ed. ac. uk/software/figtree/. The topological congruence between the trees obtained from the three loci was tested by the maximum agreement subtree (MAST) method using the online calculator of congruence index Icong  (De Vienne et al. 2007 ) available at http://max2. ese. u-psud. fr/icong/index. help. html. In order to use the information in the heterozygous nucleotide position and thus calculate more accurate estimates of molecular ITS variations among all samples (our collections and sequences from GenBank), a haplotype data set was constructed with homozygous sequences and sequences for which heterozygosity could be resolved without cloning, i.
Phylogenetic analyses and genetic diversity Partial 507-bp ITS sequences were generated from 69 samples, 522-bp tef1-α sequences from 62 samples, and 646-bp gpd sequences from 69 samples, all including two Paxillus rubicundulus samples. The ITS, tef, and gpd phylogenies support four clades in the Paxillus involutus complex and P. rubicundulus is placed as an outgroup ( Figs  1  and 2 ). According to type sequences, two of these phylogenetic species were assigned to Paxillus ammoniavirescens and Paxillus obscurisporus. A third branch, including the genome-sequenced strain ATCC 200175 (AY585913), P. involutus f. eburneus (JN673368), and an English whitish collection (JN661721), represented P. involutus. The fourth phylospecies is called Paxillus cuprinus hereafter. Phylogeny of Paxillus involutus and allies derived from the ITS data set using Bayesian analyses.
The Bayesian PPs above 0. 5 are shown above branches. The tree was rooted using sequences from P. rubicundulus. The scale shows the expected number of changes per nucleotide. Four different phylogenetically species are identified: PA = P. ammoniavirescens, PC = P. cuprinus, PI = P. involutus, PO = P. obscurisporus. All strains and gene accession numbers are presented in Tables  1  and 2. Phylogenies of Paxillus involutus and allies derived from the tef1-α (A), gpd (B), and concatenated sequences (C) using Bayesian analyses. The Bayesian PPs above 0. 5 are shown above branches. The tree was rooted using sequences from P. rubicundulus. The scale shows the expected number of changes per nucleotide. Four different phylogenetically species are identified: PA = P. ammoniavirescens, PC = P. cuprinus, PI = P.
involutus, PO = P. obscurisporus. All strains and gene accession numbers are presented in Tables  1  and 2. In the ITS tree (Fig  1 ), P. cuprinus and P. involutus on the one hand and P. ammoniavirescens and P. obscurisporus on the other hand are sister-groups. The tef tree ( Fig  2A ) reveals four wellsupported branches where P. ammoniavirescens, P. obscurisporus, and P. involutus are clustered while P. cuprinus is more distant. In the gpd tree ( Fig 2B  ), P. involutus is the most distant while P. cuprinus and P. obscurisporus are related. However, nodes are weakly supported and congruence of the three trees was confirmed (Icong = 2. 95-3, P value = 2. 45 E -17 -9. 47 E -16 ). The tree obtained with the three concatenated genes (Fig  2C ) is similar to the ITS tree. Each specimen was consistently assigned to the same phylogenetic species.
As most of the ITS sequences contained only one heterozygous position, it was possible to generate a haplophase data set, with sequences from this study and from GenBank. The numbers of ITS haplotypes were four for P. cuprinus, seven for P. involutus, nine for P. ammoniavirescens, and five for P. obscurisporus. ITS nucleotide diversity (π), which represents sequence variation, ranged between 0. 008 (PA-PO) and 0. 023 (PA-PC) at the intergroup level but ranged between 0. 001 (P. cuprinus) and 0. 003 (P. ammoniavirescens) at the intragroup level ( Table  3 ). Table  3. Statistical data calculated at the intra and interspecific levels for the four phylogenetic species (PA = P. ammoniavirescens; PC = P. cuprinus; PI = P. involutus; PO = P. obscurisporus) with the ITS haplophase data set. Genetic diversity analysis of the ITS data set (Table  3 ) indicated that P.
Discussion In this study, we combined molecular and taxonomic approaches and we included available data from the literature and from sequence databases as much as possible to clearly characterize species belonging to the Paxillus involutus complex. The phylogenetic analysis conducted with three genes (ITS, tef1-α, and gpd) and with the concatenated data set revealed four lineages, in accordance with the results obtained by Hedh et al. (2008)  with a set of five different genes (hydA, actA, rabA, gpiA, and β-tubA) and Vellinga et al. (2012). As intralineage genetic diversity was always lower than interlineage genetic diversity, the delimitation of the four species is very well supported. The tef and gpd trees do not recover the same topological relations as the ITS or concatenated trees but a similar result was also obtained with the gene hydA  ( Hedh et al.
cuprinus, contrasting with the high genetic variability of P. ammoniavirescens. These differences are supported by intraspecific genetic variations (π) calculated on a concatenated data set (1893 bp) generated from five other genes  ( Hedh et al. 2008). Actually, our π values are in accordance with those of 0. 0009 and 0. 01 calculated for group IV (P. cuprinus) and for group III (P. ammoniavirescens), respectively  ( Hedh et al. 2008). We can hypothesize that these two species have different dispersal and colonisation patterns in connection with adaptive ability. Paxillus ammoniavirescens could have features of pioneer and/or ruderal species that invest in sexual reproduction and spore production to colonise open areas, leading to a great genetic diversity. In contrast, P. cuprinus, like host-specific species such as Tricholoma populinum  ( Gryta et al.
Acknowledgements We thank all the people who helped us collect specimens:  Pierre-Arthur Moreau  (Lil12 collection and Sowerby's plate),  Guy Durrieu  (Pou09 collection),  Syméon Pitois  (SVB08 collection),  Nathalie Séjalon-Delmas  (Auz08 collection),  Giampaolo Simonini  (TO AVP164 collection), and  L3  BOPE students ( Arf08 ,  Arf09 ,  Arf12 ,  Car10 , SCV09 collections). Comments and suggestions by  Pierre-Arthur Moreau  were very helpful to improve the manuscript. We also thank  Laëtitia Buisson  for her advices for statistical analyses. Special thanks are addressed to  Annie Buchwalter  for proof-reading English language. The  Université Toulouse III Paul Sabatier , the  Centre National de la Recherche Scientifique (CNRS) , and the labex TULIP provided financial support for this study.
Collec tion Year of samp ling Locatio n Environ ment type Recorded trees Altit ude Isolat es P S a Herbari um number b Accession number ITS tef gpd of samp ling 2008 Alz12 2012 ALB0 8 Arf08 2008 Arf09 2009 Arf12 2012 Auc12 2012 Auz08 2008 KF26 Collec Locatio n Environ ment type Recorded trees Altit ude Isolat es P S a Herbari um number b Accession number ITS tef gpd Amélie-les-Bains, Pyrénée s-Oriental es, France River bank Populus, Alnus 230 m ALB0 8. 1 P A KF26 1492 KF26 1423 ALB0 8. 4 P A KF26 1354 KF26 1493 KF26 1424 ALB0 8. 6 P A KF26 1425 ALB0 8. 7 P A KF26 1426 Alzen, Ariège, France Forest Betula, Fagus 720 m Alz12. 1 PI B12112 3 KF26 1494 KF26 1427 Arfons, Tarn, France nd nd 754 m Arf08. 1 PI MN08. 1 KF26 1355 KF26 1495 KF26 1428 Arf08. 5 P C MN08. 5 KF26 1356 KF26 1496 KF26 1429 Arfons, Tarn, France nd nd 754 m Arf09.
1 P C MN09. 1 KF26 1357 KF26 1497 KF26 1430 Arf09. 2 PI MN09. 2 KF26 1358 KF26 1498 KF26 1431 Arfons, Tarn, France nd nd 754 m Arf12. 4 PI MN12. 4 KF26 1359 KF26 1432 Arf12. 8 P C MN12. 8 KF26 1360 KF26 1433 Auch, Gers, France River bank Alnus 133 m Auc12. 1 P R B12101 4 KF26 1361 KF26 1499 KF26 1434 Auzevil le-Tolosan e, Haute-Garonn e, France City park Betula, Pinus 153 m Auz08. 15 P A KF26 1362 KF26 1500 tion Year of samp ling Locatio n Environ ment type Recorded trees Altit ude Isolat es P S a Herbari um number b Accession number ITS tef gpd Auz08. 33 P A KF26 1436 Bel09 Belcaire , Aude, France Forest Picea 1050 m Bel09. 1 PI KF26 1363 KF26 1501 KF26 1437 Bel10 Belcaire , Aude, France Forest Abies 1050 m Bel10. 2 PI KF26 1364 KF26 1502 Bel10. 3 PI KF26 1365 KF26 1503 KF26 1438 Bel10. 4 PI KF26 1366 KF26 1504 Bel12 Belcaire , Aude, France Public lawn Betula 1050 m Bel12.
1 P O B12102 9 KF26 1367 KF26 1505 KF26 1439 Bou12 Boucon ne, Haute-Garonn e, France Forest edge Quercus 240 m Bou12. 1 P A B12103 2 KF26 1506 KF26 1440 Can1 2. F Cantaou s, Hautes-Pyrénée s, France Forest Picea 590 m Can12. 1 PI B12114 0. 1 KF26 1368 KF26 1507 KF26 1441 Can12. 2 PI B12114 0. 2 KF26 1369 KF26 1508 KF26 1442 Can12. R Cantaou s, Hautes-Pyrénée s, France Roadsid e in forest Corylus 590 m Can12. 3 P C B12100 7 KF26 1370 KF26 1509 KF26 1443 Car10 Cardeil hac, Haute-Garonn e, France nd nd 491 m Car10. 1 P C Collec tion Year of samp ling Locatio n Environ ment type Recorded trees Altit ude Isolat es P S a Herbari um number b Accession number ITS tef gpd Car10. 3 PI KF26 1373 KF26 1512 KF26 1445 Car10. 4 PI KF26 1374 KF26 1513 Car10. 5 PI KF26 1375 KF26 1514 KF26 1446 Car12 2012 Cardeil hac, Haute-Garonn e, France Roadsid e in forest Quercus 491 m Car12.
1 P A B12110 1 KF26 1376 KF26 1447 Cas09 2009 Castane t-Tolosan , Haute-Garonn e, France City park Betula 156 m Cas09. 1 P C KF26 1377 KF26 1515 KF26 1448 Cas09. 3 P C KF26 1378 KF26 1516 KF26 1449 Cas10 2010 Castane t-Tolosan , Haute-Garonn e, France City park Betula 156 m Cas10. 3 P C TL127-0002 KF26 1379 KF26 1517 KF26 1450 Cas12. A 2012 Castane t-Tolosan , Haute-Garonn e City park Betula 156 m Cas12. 1 P A B12100 6 KF26 1380 KF26 1518 KF26 1451 Cas12. B 2012 Castane t-Tolosan , Haute-Garonn e, France City park Betula 156 m Cas12. 4 P C KF26 1381 KF26 1519 KF26 1452 Cas12. 5 P C B12100 5 KF26 1382 KF26 1453 Cer09 2009 Céret, Pyrénée River bank Populus, Alnus 113 m Cer09. 15 P A KF26 1383 KF26 1520 KF26 Collec tion Year of samp ling Locatio n Environ ment type Recorded trees Altit ude Isolat es P S a Herbari um number b Accession number ITS tef gpd s-Oriental es, France Eau11 Eauzes, Gers, France River bank Alnus, Salix 145 m Eau11.
C1 P C CA10. B 1 KF26 1392 KF26 1530 KF26 Collec tion Year of samp ling Locatio n Environ ment type Recorded trees Altit ude Isolat es P S a Herbari um number b Accession number ITS tef gpd es, France PM10. B 2010 Prats-de-Mollo, Pyrénée s-Oriental es, France Forest Pinus, Betula 998 m PM10. B2 PI CA10. B 2 KF26 1393 KF26 1531 PM10. B3 PI CA10. B 3 KF26 1394 KF26 1532 Pou09 2009 Pouvour ville, Haute-Garonn e, France City park Cedrus 235 m Pou09. 1 P A KF26 1395 KF26 1533 KF26 1465 Pou09. 2 P A KF26 1466 Pou09. 3 P A KF26 1467 Pun11 2011 Puntous , Hautes-Pyrénée s, France Roadsid e in forest Quercus 310 m Pun11. 1 P A B11090 5 KF26 1396 KF26 1534 KF26 1468 Ram1 0 2010 Ramonv ille-Saint-Agne, Haute-Garonn e, France City park Cedrus 160 m Ram1 0. 1 P A KF26 1397 KF26 1535 KF26 1469 Ram1 0. 2 P A KF26 1398 KF26 1536 Ram1 0.
3 P A KF26 1399 KF26 1537 Ram1 1 2011 Ramonv ille-Saint-Agne, Haute-City park Betula 160 m Ram1 1. 2 P A PTC11. 2 KF26 1400 KF26 1538 tion Year of samp ling Locatio n Herbari Accession number Environ ment type Recorded trees Altit ude Isolat es P S a um number b ITS tef gpd KF26 Collec Garonn e, France Sau09 Saurat, Ariège, France Forest Abies, Picea 1180 m Sau09. 1 PI CP09. 1 KF26 1401 KF26 1471 Sau10. F Saurat, Ariège, France Forest Abies 1180 m Sau10. 1 PI CP10. 1 KF26 1402 KF26 1539 KF26 1472 Sau10. 2 PI CP10. 2 KF26 1403 KF26 1540 Sau10. R Saurat, Ariège, France Roadsid e in forest Betula, Alnus 1150 m Sau10. 3 P C CP10. 3 KF26 1404 KF26 1541 Sau11. F Saurat, Ariège, France Forest Abies, Picea 1180 m Sau11. 1 PI CP11. 1 KF26 1405 KF26 1542 KF26 1473 Sau11. 3 PI CP11. 3 KF26 1406 KF26 1543 KF26 1474 Sau11.
Collec tion Year of samp ling Locatio n Environ ment type Recorded trees Altit ude Isolat es P S a Herbari um number b Accession number ITS tef gpd Garonn e, France Toulous e, Tou12 2012 Haute-Garonn City park Populus 150 m Tou12. 1 P A UPS12. 1 KF26 1420 KF26 1552 KF26 1490 e, France Le Vernet, Ve08 2008 Haute-Garonn River bank Alnus 167 m Ve08. 2h10 P R KF26 1421 KF26 1553 KF26 1491 e, France Vez12 2012 Vezzan o, Reggio nell'Emi lia, Italy Roadsid e in forest Ostrya, Quercus, Castanea 500 m Vez12. 1 P C TO_AV P164, 6 GS1007 KF26 1422 nd: not determinated.
Accession number Locus PS a Country Recorded trees Environment type Herbarium number Reference Jarosch & AF167691 ITS PO Germany Corylus Park Pi12 Bresinsky 1999 Jarosch & AF167692 ITS PO Germany Quercus Park PiM1 Bresinsky 1999 Jarosch & AF167693 ITS PO Germany Betula Park PiM4 Bresinsky 1999 Jarosch & AF167694 ITS PO Germany Populus Park PiM2 Bresinsky 1999 AY585910 ITS PO Sweden Populus, Fagus Public lawn SE03071001 Hedh et al. 2008 Populus, AY585911 ITS PO Sweden Cornus, Tilia, Public lawn SE03-07-1622 Hedh et al. 2008 Fagus AY585913 ITS PI Scotland Betula - ATCC 200175 Hedh et al. 2008 AY585915 ITS PA France Populus - Nau Hedh et al. 2008 AY585917 ITS PA France Quercus - Maj Hedh et al. 2008 AY585921 ITS PC Sweden Fagus, Betula Pasture SE03100501 Hedh et al. 2008 AY585922 ITS PC Sweden Picea, Betula Unmanaged lawn HW03092501 Hedh et al.
Accession number Locus PS a Country Recorded trees Environment type Herbarium number Reference EU078714 ITS PO Sweden Populus, Betula Wetland, sandfill PAO03090701 Hedh et al. 2008 EU078715 ITS PO Norway Tilia Garden lawn IA04090201 Hedh et al. 2008 EU078716 ITS PI Norway Picea, Betula Forest AT04083001 Hedh et al. 2008 EU078717 ITS PI Sweden Betula, Quercus Forest SE04071201 Hedh et al. 2008 EU078721 ITS PI Canada Betula, Populus Forest CanLH14503 Hedh et al. 2008 EU078737 ITS PI CZ - - CBS 477. 89 Hedh et al. 2008 EU078739 ITS PI Netherlands - - CBS 591. 89 Hedh et al. 2008 EU078741 ITS PA Sweden Quercus, Betula Pasture SE03100403 Hedh et al. 2008 EU078742 ITS PC Sweden Betula Public lawn PAO03090703 Hedh et al. 2008 EU078743 ITS PC Sweden Populus, Corylus Pasture SE03100401 Hedh et al. 2008 EU084665 ITS PO Germany Tilia - CH 290_98 Hedh et al.
Accession number Locus PS a Country Recorded trees Environment type Herbarium number Reference JN661717 ITS PA France Quercus and Populus - A. E. Hills 2007045 (K) Vellinga et al. JN661718 ITS PA Italy - - IB1997_0980 Vellinga et al. JN661719 ITS PA Italy Populus - M. Contu (UC) s. n. Vellinga et al. JN661721 ITS PIw England Betula - A. E. Hills 2005067 (K) Vellinga et al. JN661722 ITS PI USA, TN Picea Mountain forest TENN64458 Vellinga et al. JN661723 ITS PI USA, MI - - M. Kuo 09130703 (UC) Vellinga et al. JN661724 ITS PI England - - S. Kelly s. n. Vellinga et al. JN661725 ITS PC USA, CA Corylus, Quercus - D. Deshazer DD535 Vellinga et al. JN661726 ITS PC USA, CA Betula - E. C. Vellinga 3211b (UC) Vellinga et al. JN661727 ITS PC USA, CA Betula - E. C. Vellinga 3336 (UC) Vellinga et al. JN661728 ITS PC USA, WA Betula Park E.
Number of polymorphic informative sites Total number of variable sites ITS tef gpd ITS tef gpd Mean ITS tef gpd Mean P. ammoniavirescens 32 18 27 5 7 14 8. 67 11 8 23 14. 00 P. involutus 35 20 17 3 4 2 3. 00 5 7 9 7. 00 P. cuprinus 34 20 22 1 3 4 2. 67 4 3 7 4. 67 P. obscurisporus 19 3 3 2 nd nd nd 4 6 7 5. 67 nd: not determined. a Including GenBank sequences.
© 2014 Kowanetz et al. ; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/4. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons. org/publicdomain/zero/1. 0/) applies to the data made available in this article, unless otherwise stated.
Acknowledgements The authors would like to acknowledge the contributions of all the participants in the Oceans and  Human Health Workshop  ( Bedruthan Steps , Cornwall, UK; March 20e21, 2014) with more information available at www. ecehh. org/events/oceans-humanhealth/;and the authors of the European Marine Board White Paper on Oceans and  Human Health  (http://www. marineboard. eu/images/publications/Oceans%20and%20Human%20Health-214. pdf). Funding was provided by the  European Marine Board, Oostende, Belgium ; the  European Regional Development Fund Programme   2007  to 2013 and  European Social Fund Convergence Programme for Cornwall and the Isles of Scilly (European Centre for Environment and Human Health , the  University of Exeter Medical School, Truro, Cornwall, UK) ;  Plymouth Marine Laboratory (PML), Plymouth UK ;  Scottish Association for Marine Sciences (SAMS), Oban, Scotland ; the  Institut Francais de Recherche Pour L'exploitation de la Mer (IFREMER) ,  Nantes, France ; the  European Community 's  Seventh Framework Programme  (FP7/2007 e 2013) within the  Ocean of Tomorrow call  under Grant Agreement No.
Compartmental model of resonant dendritic tree Numerical simulations to determine the influence of complex dendritic morphologies on resonance were performed using the NEURON+Python  [37, 38]  software. In order to explore the wide range of parameters that leads to significant spatio-temporal input filtering, we performed evolutionary optimizations  [39, 40]  of abstract (cable, bipolar, multipolar, ''Y'' dendrites) model neurons (Figure  3 ) as well as morphological detailed model neurons (see Figure  4 ). Optimization by evolutionary algorithms involved two critical steps: parametrization of the model neurons so they can be systematically optimized and, the quantitative assessment of the models to guide the optimization. The parameters used for the optimization are summarized in Table  S1.
Acknowledgments Jonathan Laudanski , a dear friend and a remarkable scientist, died in a climbing accident during the final review of this paper. In his short life, Jonathan touched many hearts and minds. He left behind a young loving wife, and close friends with warm memories of his kind and happy spirit. Jonathan initially studied Physics, but became very curious and interested in Neuroscience and Philosophy. So he pursued a PhD in Neuroscience and subsequently contributed to many publications in auditory physiology and computations. In his last couple of years, he joined  Oticon Medical  to pursue applications of his work to the improvement of cochlear prostheses for the deaf. Jonathan, however, remained fascinated by, and continued to contribute insights into, computational neuroscience as demonstrated by this publication.
This work was part funded by the  European Research Council  ( ERC StG 240132 ), by an  FP7 People Initial Training Network Grant , Grant number:  PITN-GA-2009-238686  (CEREBNET), by the  Blue Brain Project  and  OISTSC , and by  Gatsby Charitable Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
BCL2DB (http://bcl2db. ibcp. fr) is a database designed to integrate data on BCL-2 family members and BH3-only proteins. These proteins control the mitochondrial apoptotic pathway and probably many other cellular processes as well. This large protein group is formed by a family of pro-apoptotic and anti-apoptotic homologs that have phylogenetic relationships with BCL-2, and by a collection of evolutionarily and structurally unrelated proteins characterized by the presence of a region of local sequence similarity with BCL-2, termed the BH3 motif. BCL2DB is monthly built, thanks to an automated procedure relying on a set of homemade profile HMMs computed from seed reference sequences representative of the various BCL-2 homologs and BH3-only proteins. The BCL2DB entries integrate data from the Ensembl, Ensembl Genomes, European Nucleotide Archive and Protein Data Bank databases and are enriched with specific information like protein classification into orthology groups and distribution of BH motifs along the sequences.
Since the discovery of the bcl-2 gene 30 years ago, intense research in various disciplines has exponentially increased the quantity of data available on the BCL-2 family and BH3-only proteins. Therefore, it is of considerable interest to use bioinformatic tools to (i) understand the various groups of proteins structurally or functionally linked to BCL-2 and their implication in diseases; (ii) bring all the available information together in a specialized database [for which we have previously developed a prototype  (4) ]. We recently proposed a novel classification scheme for BCL-2-related proteins, based on phylogenetic information and computational analysis of sequence data  (5, 6). Here, we describe an enhanced version of the BCL-2 database, a computer-annotated sequence database dedicated to BCL-2 homologous and BH3-only proteins, as well as the integrated Web interface that provides easy and efficient access to the data.
The BCL2DB database BCL2DB is available since July 2013. The release 2 comprises 1039 entries, including 880 BCL-2 homologous proteins (655 encoded by metazoan genomes and 225 from viruses) and 159 BH3-only proteins. Based on our new classification scheme, we built an automated workflow to feed BCL2DB. The workflow relies on a set of specific profile HMMs  (7)  derived from 40 reference protein sequences representative of the various orthologous subgroups present within the BCL-2-like and BH3-only groups. This computational pipeline was able to identify both close and distant homologs of BCL-2 (including viral members) as well as the known repertoire of BH3-only proteins when searching the UniProt Knowledgebase (UniProtKB)  (8). The identified sequences are then annotated to provide entries in the European Nucleotide Archive (ENA) (9) EMBL-Bank format, which is loaded into a PostgreSQL relational database management system.