Sequence Alignment, Analysis, and Bioinformatic Pipelines

2013 ◽  
pp. 59-77
Author(s):  
Fuli Yu ◽  
Cristian Coarfa
Keyword(s):  
Sequence Alignment ◽  
Alignment Analysis

scholarly journals Recognition of another member of the malignant catarrhal fever virus group: an endemic gammaherpesvirus in domestic goats

2001 ◽  
Vol 82 (1) ◽  
pp. 227-232 ◽  
Author(s):  
Hong Li ◽  
Janice Keller ◽  
Donald P. Knowles ◽  
Timothy B. Crawford
Keyword(s):  
Dna Polymerase ◽  
Sequence Alignment ◽  
Gene Sequence ◽  
Homologous Sequence ◽  
Malignant Catarrhal Fever ◽  
Polymerase Gene ◽  
Virus Sequence ◽  
Herpesvirus 1 ◽  
Alignment Analysis ◽  
Recognition Of Another

A novel gammaherpesvirus in goats that is herein tentatively designated as caprine herpesvirus-2 was identified based on the sequence of a fragment from the herpesvirus DNA polymerase gene. Sequence alignment analysis revealed that the virus sequence isolated from goats was 67% identical to the homologous sequence from alcelaphine herpesvirus-1, 71% identical to ovine herpesvirus-2 and 73% identical to a recently recognized herpesvirus causing malignant catarrhal fever in white-tailed deer. Combined serological and PCR-survey data demonstrated that this virus is endemic in goats and its transmission pattern may be similar to that of ovine herpesvirus-2 in sheep.

scholarly journals Epidemiological survey of idiopathic scoliosis and sequence alignment analysis of multiple candidate genes

2011 ◽  
Vol 36 (6) ◽  
pp. 1307-1314 ◽  
Author(s):  
Tao Yang ◽  
Quanzhang Jia ◽  
Hong Guo ◽  
Jianzhong Xu ◽  
Yun Bai ◽  
...  
Keyword(s):  
Idiopathic Scoliosis ◽  
Candidate Genes ◽  
Sequence Alignment ◽  
Epidemiological Survey ◽  
Alignment Analysis

scholarly journals The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis

2000 ◽  
Vol 9 (12) ◽  
pp. 2457-2469 ◽  
Author(s):  
Arianna Rath ◽  
Alan R. Davidson
Keyword(s):  
Sequence Alignment ◽  
Sh3 Domain ◽  
Alignment Analysis

scholarly journals PENGELOMPOKKAN SEPULUH VARIETAS TEMBAKAU (Nicotiana tabacum) BERDASARKAN KERAGAMAN RUNUTAN BASA PARSIAL GEN PMT(PUTRESCINE N-METHYLTRANSFERASE) Clustering of ten tobacco (Nicotiana tabacum) varieties based on the partial PMT (putrescine N-methyltranfera

2017 ◽  
Vol 23 (1) ◽  
pp. 36
Author(s):  
Sesanti Basuki ◽  
Sudarsono Sudarsono
Keyword(s):  
Nicotiana Tabacum ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Gene Sequence ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Multiple Sequence Alignment Analysis ◽  
Nicotine Level ◽  
Alignment Analysis ◽  
The Relationship

<p align="center">Abstrak</p><p>Gen <em>PMT</em> adalah gen penyandi enzim putresina N-metiltransferase (PMT) yang berperan dalam lintasan biosintesis nikotin pada tanaman tembakau (<em>Nicotiana tabacum</em>). Sepuluh varietas tembakau yang memiliki perbedaan tingkat kadar nikotin diuji untuk mempelajari: (1) keragaman runutan basa parsial gen <em>PMT</em> dari masing-masing varietas, dan (2) kekerabatan antara sepuluh varietas tembakau yang diuji berdasarkan keragaman runutan basa parsial gen <em>PMT</em>. Keragaman runutan basa dianalisis dengan mensejajarkan data runutan basa dari sepuluh varietas tembakau yang diuji dengan runutan basa dari <em>Ntpmt_Sindoro1</em> (JQ438825) yang telah tersimpan dalam <em>database</em><em> </em><em>genbank NCBI</em>. Hasil pensejajaran digunakan untuk menghitung matriks jarak, yang selanjutnya digunakan untuk menganalisis hubungan kekerabatan diantara sepuluh varietas tembakau. Hasil analisis memperlihatkan adanya variasi ukuran dan jumlah runutan basaparsial gen <em>PMT</em> asal sepuluh varietas tembakau yang dianalisis. Hasil analisis juga memperlihatkan bahwa runutan basa parsial gen <em>PMT</em> tersebut berasal/diturunkan dari sumber (<em>ancestor</em>) yang sama dan  terkait dengan biosintesis nikotin pada tembakau. Runutan basaparsial gen <em>PMT</em> dari sepuluh varietas yang dianalisis memisahkan antara kelompok tembakau introduksi (kadar nikotin rendah-sedang) dengan kelompok tembakau lokal (kadar nikotin sedang-tinggi). Dua kelompok memisah berdasarkan level kadar nikotin, danperbedaan/perubahan susunan basa pada situs-situs tertentu dari runutan basaparsial gen <em>PMT</em>  yang dianalisis. Informasi tentang mutasi yang terjadi pada situs-situs runutan basa dari parsial gen <em>PMT</em><em> </em>dapat digunakan untuk mempelajari keterkaitan antara perubahan basa pada fragmen gen <em>PMT</em> dengan kandungan nikotin total tembakau yang terjadi selama proses evolusi.</p><p>Kata kunci: Analisis pengelompokkan, gen <em>PMT,</em>Nikotin, <em>Nicotiana tabacum</em></p><p align="center"><strong> </strong></p><p align="center">Abstract</p><p><strong> </strong><em>PMT</em> gene is the gene encoded putrescine N-methiltransferase which is related to nicotine biosinthesis in tobacco (<em>Nicotiana  tabacum</em>). Ten tobacco varieties with different nicotine level were used inthis study. The aims of this study were: (1) to analyze thepartial <em>PMT</em> gene sequence diversity among ten tobacco varieties, and (2) to evaluate the closed-relationship amongten tobacco varieties based on their partial<em>PMT</em> gene sequences diversity.Sequence diversity was analyzed by multiple sequence alignment between the partial<em>PMT</em> gene sequence of the ten tobacco varietiesand <em>Ntpmt_Sindoro1 </em>sequence deposited in the NCBI gene-bank database.The phylogenetic relationship amongthe sequences was inferred by genetic distancebetween pairs of sequences using the pairwise and multiple sequence alignment analysis. Analysis of the sequences showed that all varieties analyzed had varied in size and number of the <em>PMT</em> gene fragments yielded. The analysis also revealed that thepartial<em>PMT</em> gene sequencesarecoming from the same ancestor which related to nicotine biosynthesis in tobacco. Phylogenetic analysis separated the partial<em>PMT</em> gene sequences into two different branches significantly (bootstrap value = 100), and clustered together based on tobacco types with different nicotine level in whichcould be due to some baseschanged on the specific sites of the<em>PMT</em> gene sequences.  This information could be used to study the relationship between some bases changed on the specific sites of the<em>PMT</em> gene sequences and the nicotine content variation yielded by the ten tobacco varieties that is happened during evolution time.</p><p>Key words: Clustering analysis, <em>PMT</em> gene, nicotine, <em>Nicotiana tabacum</em></p>

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