Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Macagno, Eduardo R ^a   Gaasterland, Terry ^a,b   Edsall, Lee ^b   Bafna, Vineet ^c   Soares, Marcelo B ^d   Scheetz, Todd ^e   Casavant, Thomas ^e   Da Silva, Corinne ^f   Wincker, Patrick ^f   Tasiemski, Aurélie ^g   Salzet, Michel ^g  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d NORTHWESTERN UNIVERSITY   (United States)

^e UNIVERSITY OF IOWA   (United States)

^f CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^g UNIV LILLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME; ANTIMICROBIAL CATIONIC PEPTIDE; CYTOKINE; LEUKOCYTE ANTIGEN; PATTERN RECOGNITION RECEPTOR; TOLL LIKE RECEPTOR;

ADAPTIVE IMMUNITY; ANIMAL TISSUE; ARTICLE; CENTRAL NERVOUS SYSTEM; COMPUTER PROGRAM; CONTROLLED STUDY; DEVELOPMENTAL STAGE; EMBRYO; EXPRESSED SEQUENCE TAG; GENE LIBRARY; GENETIC CONSERVATION; GENETIC DATABASE; IMMUNOGENETICS; INNATE IMMUNITY; INVERTEBRATE; LEECH; MOLECULAR CLONING; NONHUMAN; PROTEIN DATABASE; SEQUENCE HOMOLOGY; VERTEBRATE; ANIMAL; GENE EXPRESSION PROFILING; GENETICS; HUMAN; IMMUNOLOGY; METABOLISM; NUCLEIC ACID DATABASE; PHYSIOLOGY; PRENATAL DEVELOPMENT; REGENERATION; SPECIES DIFFERENCE;

ADAPTIVE IMMUNITY; ANIMALS; ANTIGENS, CD; ANTIMICROBIAL CATIONIC PEPTIDES; CENTRAL NERVOUS SYSTEM; CYTOKINES; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; HIRUDO MEDICINALIS; HUMANS; IMMUNITY, INNATE; RECEPTORS, PATTERN RECOGNITION; REGENERATION; RNA, MESSENGER; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TOLL-LIKE RECEPTORS;

EID: 77955098185     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-407     Document Type: Article

References (83)

1. Rados C. Beyond bloodletting: FDA gives leeches a medical makeover. FDA Consum 2004, 38(5):9.
2. Baskova IP, Zavalova LL. [Polyfunctionality of destabilase, a lysozyme from a medicinal leech]. Bioorg Khim 2008, 34(3):337-343.
3. Zavalova LL, Yudina TG, Artamonova II, Baskova IP. Antibacterial non-glycosidase activity of invertebrate destabilase-lysozyme and of its helical amphipathic peptides. Chemotherapy 2006, 52(3):158-160. 10.1159/000092904, 16636539.
4. Seymour JL, Henzel WJ, Nevins B, Stults JT, Lazarus RA. Decorsin. A potent glycoprotein IIb-IIIa antagonist and platelet aggregation inhibitor from the leech Macrobdella decora. J Biol Chem 1990, 265(17):10143-10147.
5. Chopin V, Bilfinger TV, Stefano GB, Matias I, Salzet M. Amino-acid-sequence determination and biological activity of cytin, a naturally occurring specific chymotrypsin inhibitor from the leech Theromyzon tessulatum. Eur J Biochem 1997, 249(3):733-738. 10.1111/j.1432-1033.1997.t01-1-00733.x, 9395320.
6. Chopin V, Matias I, Stefano GB, Salzet M. Amino acid sequence determination and biological activity of therin, a naturally occuring specific trypsin inhibitor from the leech Theromyzon tessulatum. Eur J Biochem 1998, 254(3):565-570. 10.1046/j.1432-1327.1998.2540565.x, 9688267.
7. Chopin V, Salzet M, Baert J, Vandenbulcke F, Sautiere PE, Kerckaert JP, Malecha J. Therostasin, a novel clotting factor Xa inhibitor from the rhynchobdellid leech, Theromyzon tessulatum. J Biol Chem 2000, 275(42):32701-32707. 10.1074/jbc.M909217199, 10852926.
8. Chopin V, Stefano G, Salzet M. Biochemical evidence of specific trypsin-chymotrypsin inhibitors in the rhynchobdellid leech, Theromyzon tessulatum. J Enzyme Inhib 2000, 15(4):367-379.
9. Salzet M, Chopin V, Baert J, Matias I, Malecha J. Theromin, a novel leech thrombin inhibitor. J Biol Chem 2000, 275(40):30774-30780. 10.1074/jbc.M000787200, 10837466.
10. Tasiemski A, Vandenbulcke F, Mitta G, Lemoine J, Lefebvre C, Sautiere PE, Salzet M. Molecular characterization of two novel antibacterial peptides inducible upon bacterial challenge in an annelid, the leech Theromyzon tessulatum. J Biol Chem 2004, 279(30):30973-30982. 10.1074/jbc.M312156200, 15102860.
11. Tasiemski A, Verger-Bocquet M, Cadet M, Goumon Y, Metz-Boutigue MH, Aunis D, Stefano GB, Salzet M. Proenkephalin A-derived peptides in invertebrate innate immune processes. Brain Res Mol Brain Res 2000, 76(2):237-252. 10.1016/S0169-328X(00)00005-X, 10762699.
12. Salzet M. Leech thrombin inhibitors. Curr Pharm Des 2002, 8(7):493-503. 10.2174/1381612023395664, 11945154.
13. Salzet M, Macagno ER. Recent Advances on Development, Regeneration and Immune Responses of the Leech Nervous System. Annelids as Models Systems in the Biological Sciences 2009, 156-185. Wiley Blackwell, Dan Shain.
14. Blackshaw SE, Babington EJ, Emes RD, Malek J, Wang WZ. Identifying genes for neuron survival and axon outgrowth in Hirudo medicinalis. J Anat 2004, 204(1):13-24. 10.1111/j.1469-7580.2004.00260.x, 1571235, 14690474.
15. Korneev S, Fedorov A, Collins R, Blackshaw SE, Davies JA. A subtractive cDNA library from an identified regenerating neuron is enriched in sequences up-regulated during nerve regeneration. Invert Neurosci 1997, 3(2-3):185-192. 10.1007/BF02480373, 9783443.
16. Schikorski D, Cuvillier-Hot V, Leippe M, Boidin-Wichlacz C, Slomianny C, Macagno E, Salzet M, Tasiemski A. Microbial challenge promotes the regenerative process of the injured central nervous system of the medicinal leech by inducing the synthesis of antimicrobial peptides in neurons and microglia. J Immunol 2008, 181(2):1083-1095. 2872924, 18606660.
17. Schikorski D, Cuvillier-Hot V, Boidin-Wichlacz C, Slomianny C, Salzet M, Tasiemski A. Deciphering the immune function and regulation by a TLR of the cytokine EMAPII in the lesioned central nervous system using a leech model. J Immunol 2009, 183(11):7119-7128. 10.4049/jimmunol.0900538, 19917687.
18. Tahtouh M, Croq F, Vizioli J, Sautiere PE, Van Camp C, Salzet M, Daha MR, Pestel J, Lefebvre C. Evidence for a novel chemotactic C1q domain-containing factor in the leech nerve cord. Mol Immunol 2009, 46(4):523-531. 10.1016/j.molimm.2008.07.026, 18952286.
19. Vergote D, Macagno ER, Salzet M, Sautiere PE. Proteome modifications of the medicinal leech nervous system under bacterial challenge. Proteomics 2006, 6(17):4817-4825. 10.1002/pmic.200500902, 16888763.
20. Vergote D, Sautiere PE, Vandenbulcke F, Vieau D, Mitta G, Macagno ER, Salzet M. Up-regulation of neurohemerythrin expression in the central nervous system of the medicinal leech, Hirudo medicinalis, following septic injury. J Biol Chem 2004, 279(42):43828-43837. 10.1074/jbc.M403073200, 15258158.
21. Baker MW, Macagno ER. RNAi of the receptor tyrosine phosphatase HmLAR2 in a single cell of an intact leech embryo leads to growth-cone collapse. Curr Biol 2000, 10(17):1071-1074. 10.1016/S0960-9822(00)00674-6, 10996077.
22. Baker MW, Macagno ER. Characterizations of Hirudo medicinalis DNA promoters for targeted gene expression. J Neurosci Methods 2006, 156(1-2):145-153. 10.1016/j.jneumeth.2006.02.026, 16621015.
23. Shefi O, Simonnet C, Baker MW, Glass JR, Macagno ER, Groisman A. Microtargeted gene silencing and ectopic expression in live embryos using biolistic delivery with a pneumatic capillary gun. J Neurosci 2006, 26(23):6119-6123. 10.1523/JNEUROSCI.1237-06.2006, 16763019.
24. Wisztorski M, Croix D, Macagno E, Fournier I, Salzet M. Molecular MALDI imaging: An emerging technology for neuroscience studies. Dev Neurobiol 2008, 68(6):845-858. 10.1002/dneu.20623, 18383549.
25. Macagno ER. Number and distribution of neurons in leech segmental ganglia. J Comp Neurol 1980, 190(2):283-302. 10.1002/cne.901900206, 7381060.
26. Sawyer RT. Leech biology and behaviour. 1986, Clarendon Press, Oxford, England, I, II, III.
27. Baptista CA, Gershon TR, Macagno ER. Peripheral organs control central neurogenesis in the leech. Nature 1990, 346(6287):855-858. 10.1038/346855a0, 2392152.
28. Kristan WB, Lockery SR, Lewis JE. Using reflexive behaviors of the medicinal leech to study information processing. J Neurobiol 1995, 27(3):380-389. 10.1002/neu.480270310, 7673896.
29. Briggman KL, Kristan WB. Imaging dedicated and multifunctional neural circuits generating distinct behaviors. J Neurosci 2006, 26(42):10925-10933. 10.1523/JNEUROSCI.3265-06.2006, 17050731.
30. Soares MB, de Fatima Bonaldo M, Hackett JD, Bhattacharya D. Expressed sequence tags: normalization and subtraction of cDNA libraries expressed sequence tags\normalization and subtraction of cDNA libraries. Methods Mol Biol 2009, 533:109-122.
31. Siddall ME, Trontelj P, Utevsky SY, Nkamany M, Macdonald KS. Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis. Proc Biol Sci 2007, 274(1617):1481-1487. 10.1098/rspb.2007.0248, 2176162, 17426015.
32. Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB. An RNA map predicting Nova-dependent splicing regulation. Nature 2006, 444(7119):580-586. 10.1038/nature05304, 17065982.
33. Taneri B, Snyder B, Novoradovsky A, Gaasterland T. Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. Genome Biol 2004, 5(10):R75. 10.1186/gb-2004-5-10-r75, 545595, 15461794.
34. Frobius AC, Seaver EC. Capitella sp. I homeobrain-like, the first lophotrochozoan member of a novel paired-like homeobox gene family. Gene Expr Patterns 2006, 6(8):985-991. 10.1016/j.modgep.2006.04.002, 16765105.
35. Moroz LL, Edwards JR, Puthanveettil SV, Kohn AB, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, et al. Neuronal transcriptome of aplysia: neuronal compartments and circuitry. Cell 2006, 127(7):1453-1467. 10.1016/j.cell.2006.09.052, 17190607.
36. Lee YS, Choi SL, Kim TH, Lee JA, Kim HK, Kim H, Jang DJ, Lee JJ, Lee S, Sin GS, et al. Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai. Proc Natl Acad Sci USA 2008, 105(47):18602-18607. 10.1073/pnas.0808893105, 2587617, 19017802.
37. Feng ZP, Zhang Z, van Kesteren RE, Straub VA, van Nierop P, Jin K, Nejatbakhsh N, Goldberg JI, Spencer GE, Yeoman MS, et al. Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis. BMC Genomics 2009, 10:451. 10.1186/1471-2164-10-451, 2760584, 19775440.
38. Taft AS, Vermeire JJ, Bernier J, Birkeland SR, Cipriano MJ, Papa AR, McArthur AG, Yoshino TP. Transcriptome analysis of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE). Parasitology 2009, 136(5):469-485. 10.1017/S0031182009005733, 19265565.
39. Balavoine G. [The upside-down origin of chordates supported by non-chordate studies]. Med Sci (Paris) 2007, 23(11):1027-1028.
40. Denes AS, Jekely G, Steinmetz PR, Raible F, Snyman H, Prud'homme B, Ferrier DE, Balavoine G, Arendt D. Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria. Cell 2007, 129(2):277-288. 10.1016/j.cell.2007.02.040, 17448990.
41. Kerner P, Hung J, Behague J, Le Gouar M, Balavoine G, Vervoort M. Insights into the evolution of the snail superfamily from metazoan wide molecular phylogenies and expression data in annelids. BMC Evol Biol 2009, 9:94. 10.1186/1471-2148-9-94, 2688512, 19426549.
42. Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, et al. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. Science 2005, 310(5752):1325-1326. 10.1126/science.1119089, 16311335.
43. Prud'homme B, de Rosa R, Arendt D, Julien JF, Pajaziti R, Dorresteijn AW, Adoutte A, Wittbrodt J, Balavoine G. Arthropod-like expression patterns of engrailed and wingless in the annelid Platynereis dumerilii suggest a role in segment formation. Curr Biol 2003, 13(21):1876-1881. 10.1016/j.cub.2003.10.006, 14588243.
44. Prud'homme B, Lartillot N, Balavoine G, Adoutte A, Vervoort M. Phylogenetic analysis of the Wnt gene family. Insights from lophotrochozoan members. Curr Biol 2002, 12(16):1395. 10.1016/S0960-9822(02)01068-0, 12194820.
45. Janeway CA. The immune system evolved to discriminate infectious nonself from noninfectious self. Immunol Today 1992, 13(1):11-16. 10.1016/0167-5699(92)90198-G, 1739426.
46. Janeway CA, Medzhitov R. Introduction: the role of innate immunity in the adaptive immune response. Semin Immunol 1998, 10(5):349-350. 10.1006/smim.1998.0142, 9799708.
47. McLean JA, Ridenour WB, Caprioli RM. Profiling and imaging of tissues by imaging ion mobility-mass spectrometry. J Mass Spectrom 2007, 42(8):1099-1105. 10.1002/jms.1254, 17621390.
48. Medzhitov R, Janeway C. Innate immune recognition: mechanisms and pathways. Immunol Rev 2000, 173:89-97. 10.1034/j.1600-065X.2000.917309.x, 10719670.
49. Medzhitov R, Janeway CA. Innate immunity: impact on the adaptive immune response. Curr Opin Immunol 1997, 9(1):4-9. 10.1016/S0952-7915(97)80152-5, 9039775.
50. Medzhitov R, Janeway CA. Innate immune induction of the adaptive immune response. Cold Spring Harb Symp Quant Biol 1999, 64:429-435. 10.1101/sqb.1999.64.429, 11232318.
51. Medzhitov R, Preston-Hurlburt P, Janeway CA. A human homologue of the Drosophila Toll protein signals activation of adaptive immunity. Nature 1997, 388(6640):394-397. 10.1038/41131, 9237759.
52. Homma S, Shimada T, Hikake T, Yaginuma H. Expression pattern of LRR and Ig domain-containing protein (LRRIG protein) in the early mouse embryo. Gene Expr Patterns 2009, 9(1):1-26. 10.1016/j.gep.2008.09.004, 18848646.
53. Bergman P, Termen S, Johansson L, Nystrom L, Arenas E, Jonsson AB, Hokfelt T, Gudmundsson GH, Agerberth B. The antimicrobial peptide rCRAMP is present in the central nervous system of the rat. J Neurochem 2005, 93(5):1132-1140. 10.1111/j.1471-4159.2005.03081.x, 15934934.
54. Martin F, Dimasi N, Volpari C, Perrera C, Di Marco S, Brunetti M, Steinkuhler C, De Francesco R, Sollazzo M. Design of selective eglin inhibitors of HCV NS3 proteinase. Biochemistry 1998, 37(33):11459-11468. 10.1021/bi980283w, 9708981.
55. Auerswald EA, Morenweiser R, Sommerhoff CP, Piechottka GP, Eckerskorn C, Gurtler LG, Fritz H. Recombinant leech-derived tryptase inhibitor: construction, production, protein chemical characterization and inhibition of HIV-1 replication. Biol Chem Hoppe Seyler 1994, 375(10):695-703.
56. Murray JC, Heng YM, Symonds P, Rice K, Ward W, Huggins M, Todd I, Robins RA. Endothelial monocyte-activating polypeptide-II (EMAP-II): a novel inducer of lymphocyte apoptosis. J Leukoc Biol 2004, 75(5):772-776. 10.1189/jlb.1003487, 14982944.
57. de Eguileor M, Grimaldi A, Tettamanti G, Valvassori R, Cooper EL, Lanzavecchia G. Lipopolysaccharide-dependent induction of leech leukocytes that cross-react with vertebrate cellular differentiation markers. Tissue Cell 2000, 32(5):437-445. 10.1054/tice.2000.0132, 11201283.
58. de Eguileor M, Grimaldi A, Tettamanti G, Valvassori R, Cooper EL, Lanzavecchia G. Different types of response to foreign antigens by leech leukocytes. Tissue Cell 2000, 32(1):40-48. 10.1054/tice.1999.0085, 10798316.
59. Akamatsu Y, Oettinger MA. Distinct roles of RAG1 and RAG2 in binding the V(D)J recombination signal sequences. Mol Cell Biol 1998, 18(8):4670-4678. 109053, 9671477.
60. van Gent DC, Ramsden DA, Gellert M. The RAG1 and RAG2 proteins establish the 12/23 rule in V(D)J recombination. Cell 1996, 85(1):107-113. 10.1016/S0092-8674(00)81086-7, 8620529.
61. Panchin Y, Moroz LL. Molluscan mobile elements similar to the vertebrate Recombination-Activating Genes. Biochem Biophys Res Commun 2008, 369(3):818-823. 10.1016/j.bbrc.2008.02.097, 2719772, 18313399.
62. Fugmann SD, Messier C, Novack LA, Cameron RA, Rast JP. An ancient evolutionary origin of the Rag1/2 gene locus. Proc Natl Acad Sci USA 2006, 103(10):3728-3733. 10.1073/pnas.0509720103, 1450146, 16505374.
63. Hibino T, Loza-Coll M, Messier C, Majeske AJ, Cohen AH, Terwilliger DP, Buckley KM, Brockton V, Nair SV, Berney K, et al. The immune gene repertoire encoded in the purple sea urchin genome. Dev Biol 2006, 300(1):349-365. 10.1016/j.ydbio.2006.08.065, 17027739.
64. Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006, 314(5801):941-952. 10.1126/science.1133609, 17095691.
65. Wilson DR, Norton DD, Fugmann SD. The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails. Dev Comp Immunol 2008, 32(10):1221-1230. 10.1016/j.dci.2008.03.012, 2518978, 18499250.
66. Kapitonov VV, Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 2005, 3(6):e181. 10.1371/journal.pbio.0030181, 1131882,1131882, 15898832.
67. Chen S, Li X. Molecular characterization of the first intact Transib transposon from Helicoverpa zea. Gene 2008, 408(1-2):51-63. 10.1016/j.gene.2007.10.015, 18031956.
68. Hanelt B, Lun CM, Adema CM. Comparative ORESTES-sampling of transcriptomes of immune-challenged Biomphalaria glabrata snails. J Invertebr Pathol 2008, 99(2):192-203. 10.1016/j.jip.2008.06.002, 2724063, 18590737.
69. Lockyer AE, Spinks JN, Walker AJ, Kane RA, Noble LR, Rollinson D, Dias-Neto E, Jones CS. Biomphalaria glabrata transcriptome: identification of cell-signalling, transcriptional control and immune-related genes from open reading frame expressed sequence tags (ORESTES). Dev Comp Immunol 2007, 31(8):763-782. 10.1016/j.dci.2006.11.004, 1871615,1871615, 17208299.
70. Mitta G, Galinier R, Tisseyre P, Allienne JF, Girerd-Chambaz Y, Guillou F, Bouchut A, Coustau C. Gene discovery and expression analysis of immune-relevant genes from Biomphalaria glabrata hemocytes. Dev Comp Immunol 2005, 29(5):393-407. 10.1016/j.dci.2004.10.002, 15707661.
71. Vergote D, Bouchut A, Sautiere PE, Roger E, Galinier R, Rognon A, Coustau C, Salzet M, Mitta G. Characterisation of proteins differentially present in the plasma of Biomphalaria glabrata susceptible or resistant to Echinostoma caproni. Int J Parasitol 2005, 35(2):215-224. 10.1016/j.ijpara.2004.11.006, 15710442.
72. McTaggart SJ, Conlon C, Colbourne JK, Blaxter ML, Little TJ. The components of the Daphnia pulex immune system as revealed by complete genome sequencing. BMC Genomics 2009, 10:175. 10.1186/1471-2164-10-175, 2685406, 19386092.
73. Tirape A, Bacque C, Brizard R, Vandenbulcke F, Boulo V. Expression of immune-related genes in the oyster Crassostrea gigas during ontogenesis. Dev Comp Immunol 2007, 31(9):859-873. 10.1016/j.dci.2007.01.005, 17337052.
74. Wang L, Song L, Zhao J, Qiu L, Zhang H, Xu W, Li H, Li C, Wu L, Guo X. Expressed sequence tags from the zhikong scallop (Chlamys farreri): discovery and annotation of host-defense genes. Fish Shellfish Immunol 2009, 26(5):744-750. 10.1016/j.fsi.2009.03.002, 19328855.
75. Fernandez J, Stent GS. Embryonic development of the hirudinid leech Hirudo medicinalis: structure, development and segmentation of the germinal plate. J Embryol Exp Morphol 1982, 72:71-96.
76. Bonaldo MF, Lennon G, Soares MB. Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 1996, 6(9):791-806. 10.1101/gr.6.9.791, 8889548.
77. Scheetz TE, Zabner J, Welsh MJ, Coco J, Eyestone Mde F, Bonaldo M, Kucaba T, Casavant TL, Soares MB, McCray PB. Large-scale gene discovery in human airway epithelia reveals novel transcripts. Physiol Genomics 2004, 17(1):69-77. 10.1152/physiolgenomics.00188.2003, 14701920.
78. Scheetz TE, Laffin JJ, Berger B, Holte S, Baumes SA, Brown R, Chang S, Coco J, Conklin J, Crouch K, et al. High-throughput gene discovery in the rat. Genome Res 2004, 14(4):733-741. 10.1101/gr.1414204, 383320, 15060017.
79. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8(3):175-185.
80. Scheetz TE, Trivedi N, Roberts CA, Kucaba T, Berger B, Robinson NL, Birkett CL, Gavin AJ, O'Leary B, Braun TA, et al. ESTprep: preprocessing cDNA sequence reads. Bioinformatics 2003, 19(11):1318-1324. 10.1093/bioinformatics/btg159, 12874042.
81. Smit A, Hubley R, Green P. RepeatMasker Open-3.0. 1996, , http://www.repeatmasker.org
82. Scheetz T, Trivedi N, Pedretti KT, Braun TA, Casavant TL. Gene transcript clustering: a comparison of parallel approaches. Future Generation Computer Systems 2005, 21(5):731-735.
83. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.