Organizing hematologic gene sequence data using neighbor joining phylogeny method

  • Authors

    • B J. Bipin Nair
    2018-05-29
    https://doi.org/10.14419/ijet.v7i2.31.13387
  • Paralogous gene, orhtologous gene, neighbor joining tree, neighbor joining method.

  • Abstract

    There are a number of methods to spot orthologous genes from homologous genes. Since identifying orthologous genes are main problem and play a major role in the hematologic genetic disorders. In this paper, we propose different approaches to discover orthologs of homologous hereditary diseases of the hematological system and find the evolutionary relationship between hereditary genetic diseases of the hematological system by adjoining the joining method of contiguous merging trees.

     

  • References

    1. [1] Wong KC & Zhang Z, “SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequencesâ€, Bioinformatics, (2014).

      [2] Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F & Perrière, G, “Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databasesâ€, Bioinformatics, Vol.21, No.11,(2005), pp.2596-2603.

      [3] Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL & Herrero J, “Toward community standards in the quest for orthologsâ€, Bioinformatics, Vol.28, No.6,(2012), pp.900-904.

      [4] Chen R & Jeong SS, “Functional prediction: identification of protein orthologs and paralogsâ€, Protein Science, Vol.9, No.12, (2000), pp.2344-2353.

      [5] Cannon SB & Young ND, “OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogeniesâ€, BMC bioinformatics, Vol.4, No.1,(2003).

      [6] Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM & DeSalle R “OrthologID: automation of genome-scale ortholog identification within a parsimony frameworkâ€, Bioinformatics, Vol.22, No.6,(2006), pp.699-707.

      [7] Sonnhammer EL, Gabaldón T, da Silva AWS, Martin M, Robinson-Rechavi M, Boeckmann B & Dessimoz C, “Big data and other challenges in the quest for orthologsâ€, Bioinformatics , (2014).

      [8] Li YI & Copley RR, “Scaffolding low quality genomes using orthologous protein sequencesâ€, Bioinformatics, Vol.29, No.2,(2013), pp.160-165.

      [9] Kim K, Kim W & Kim S, “ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithmsâ€, Bioinformatics, Vol.27, No.12,(2011), pp.1731-1733.

      [10] Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC & Sali, A, “Evolutionary constraints on structural similarity in orthologs and paralogsâ€, Protein Science, Vol.18, No.6,(2009), pp.1306-1315.

      [11] Mahmood K, Konagurthu AS, Song J, Buckle AM, Webb GI & Whisstock JC, “EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomesâ€, Bioinformatics, Vol.26, No.17,(2010), pp.2076-2084.

      [12] Forslund K & Sonnhammer EL, “Benchmarking homology detection procedures with low complexity filtersâ€, Bioinformatics, Vol.25, No.19,(2009), pp.2500-2505.

      [13] Yosef N, Sharan R & Noble WS, “Improved network-based identification of protein orthologsâ€, Bioinformatics, Vol.24, No.16, (2008), pp.i200-i206.

      [14] Storm CE & Sonnhammer EL, “Automated Ortholog inference from phylogenetic trees and Calculatio of orthologyreliabilityâ€, Bioinformatics, Vol.18, No.1, (2002), pp.92-99.

      [15] Alexeyenko A, Tamas I, Liu G & Sonnhammer EL, “Automatic clustering of orthologs and Inparalo shared by multiple proteomesâ€, Bioinformatics, Vol.22, No.14,(2006), pp.e9-e15.

      [16] DeLuca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S & Wall DP, “Roundup: a multi-genome repository of orthologs and evolutionary distancesâ€, Bioinformatics, Vol.22, No.16, (2006), pp.2044-2046.

      [17] Moreno-Hagelsieb G & Latimer K, “Choosing BLAST options for better detection of orthologs as reciprocal best hitsâ€, Bioinformatics, Vol.24, No.3,(2008), pp.319-324.

      [18] Arvestad L, Berglund AC, Lagergren J & Sennblad B, “Bayesian gene/species tree reconciliation and orthology analysis using MCMCâ€, Bioinformatics, Vol.19, (2003), pp.i7-i15.

      [19] Bipin Nair BJ, Sujith M & Alphonsa MV, “Self-regulating Exploration for Orthologous in Homologous Hematologic Gene Sequence Data Using UPGMA Methodâ€, IJET, Vol.8, No.1, (2016), pp.287-292.

  • Downloads

  • How to Cite

    J. Bipin Nair, B. (2018). Organizing hematologic gene sequence data using neighbor joining phylogeny method. International Journal of Engineering & Technology, 7(2.31), 13-15. https://doi.org/10.14419/ijet.v7i2.31.13387

    Received date: 2018-05-28

    Accepted date: 2018-05-28

    Published date: 2018-05-29