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Author(s):  
Kartika Senjarini ◽  
Lailly Nur Uswatul Hasanah ◽  
Miatin Alvin Septianasari ◽  
Muhammad Khalid Abdullah ◽  
Rike Oktarianti ◽  
...  

The presence of intraspecies variations of An. vagus later categorized as the subspecies of An. vagus vagus and An. vagus limosus, could be an obstacle to the identification process, which is an important step for malaria vector’s competence characterization. Based on morphological identification, those subspecies could be distinguished by the presences of pale scales in prehumeral and pale bands  in proboscis. The objective of this research was to compare subspecies complexes of An. vagus morphologically and molecularly using Internal Transcribed Spacer 2 (ITS2). Anopheles samples were collected from Bangsring, Banyuwangi. Their phylogenetic tree was constructed by using NJ method based on their ITS2 sequences. BLAST result showed that An. vagus vagus and An. vagus limosus were similar to An. vagus FJ654649.1 from East Java Indonesia and East Timor based on its 99% homology and their molecular distance. The Neighbour Joining (NJ) tree grouped those subspecies in one clade with a boostrap value of 82%. This subspeciation might be due to the different rates of evolution. ITS2 sequences of An. vagus vagus and An. vagus limosus were submitted to GenBank with the accession number of MW314227.1 and MW319822.1, respectively. Kemunculan variasi intraspesies An. vagus yang kemudian dikategorikan sebagai subspesies An. vagus vagus dan An. vagus limosus menjadi kendala dalam proses identifikasi yang merupakan langkah penting dalam menentukan kompetensi vektor malaria. Berdasarkan karakter morfologi, subspesies tersebut dibedakan dengan adanya sisik pucat pada bagian prehumeral dan pita pucat pada probosis. Penelitian ini bertujuan untuk membandingkan subspesies An. vagus secara morfologis dan molekuler menggunakan Internal Transcribed Spacer 2 (ITS2). Nyamuk Anopheles didapatkan dari Bangsring, Banyuwangi. Konstruksi pohon filogeni dilakukan berdasarkan sekuen ITS2 yang dianalisis menggunakan metode NJ. Hasil BLAST menunjukkan, ITS2 An. vagus vagus dan An. vagus limosus memiliki tingkat homologi 99% dan jarak evolusi molekuler terendah dengan An. vagus FJ654649.1 dari Jawa Timur Indonesia dan Timor Timur. Pohon NJ mengelompokkan subspesies tersebut dalam satu klade dengan nilai boostrap 82%. Hal ini dapat terjadi karena perbedaan kecepatan evolusi yang memungkinkan terjadinya subspesiasi. Urutan basa ITS2 dari An. vagus vagus dan An. vagus limosus telah didaftarkan ke GenBank dengan nomor aksesi MW314227.1 dan MW319822.1.


2021 ◽  
Vol 9 (1) ◽  
pp. 13-20
Author(s):  
Cynthia Dewi Gaina ◽  
Frits B. H. Francis

The Sumba horse is one of the local horses in Indonesia which is known as racing horse Several candidate genes are known to influence the outward characteristics of the Sumba racehorse, which play main role in the development of the horse's muscles from embryo to adulthood. This research aims to identify candidate genes for the Sumba racehorse in stallion and mares. Blood samples from 5 stallions and 5 mares were collected and analyzed. The method used in this research was by using polymerase chain reaction (PCR), electrophoresis and DNA sequencing. The results of DNA amplification fragments at a temperature of 600c showed a fragment size of 463 bp. A total of 10 samples were sequenced on the PCR machine. The forward primer was 5'-TATTCTTCTTGGGAGGGAGGACTACT-3 'and reverse primer was 5'-GCAAGTAATTAGCACAAAAATTTGAATG-3'. The obtained data was analyzed using the Basic Local Alignment Sealing Tool (BLAST). Result of this study could be used as an initial identification of candidate genes for racing activity in stallion and mares that can complement the selection of racing horses.


PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0243271 ◽  
Author(s):  
Joseph Ojonugwa Shaibu ◽  
Chika K. Onwuamah ◽  
Ayorinde Babatunde James ◽  
Azuka Patrick Okwuraiwe ◽  
Olufemi Samuel Amoo ◽  
...  

In an outbreak, effective detection of the aetiological agent(s) involved using molecular techniques is key to efficient diagnosis, early prevention and management of the spread. However, sequencing is necessary for mutation monitoring and tracking of clusters of transmission, development of diagnostics and for vaccines and drug development. Many sequencing methods are fast evolving to reduce test turn-around-time and to increase through-put compared to Sanger sequencing method; however, Sanger sequencing remains the gold standard for clinical research sequencing with its 99.99% accuracy This study sought to generate sequence data of SARS-CoV-2 using Sanger sequencing method and to characterize them for possible site(s) of mutations. About 30 pairs of primers were designed, synthesized, and optimized using endpoint PCR to generate amplicons for the full length of the virus. Cycle sequencing using BigDye Terminator v.3.1 and capillary gel electrophoresis on ABI 3130xl genetic analyser were performed according to the manufacturers’ instructions. The sequence data generated were assembled and analysed for variations using DNASTAR Lasergene 17 SeqMan Ultra. Total length of 29,760bp of SARS-CoV-2 was assembled from the sample analysed and deposited in GenBank with accession number: MT576584. Blast result of the sequence assembly shows a 99.97% identity with the reference sequence. Variations were noticed at positions: nt201, nt2997, nt14368, nt16535, nt20334, and nt28841-28843, which caused amino acid alterations at the S (aa614) and N (aa203-204) regions. The mutations observed at S and N-gene in this study may be indicative of a gradual changes in the genetic coding of the virus hence, the need for active surveillance of the viral genome.


2020 ◽  
Vol 51 (6) ◽  
pp. 1534-1542
Author(s):  
Abbas & et al.

This study was aimed to identify dermatophytic selective isolate using PCR technique as a rapid molecular assay. The results of this study showed among 60 samples of patients suffering from ringworm  disease. forty isolates (66%) were Trichophyton  mentagrophytes  which diagnosed as dermatophytosis according to morphological and cultural methods. In order to investigate the ability of isolates to keratin analyses using solid medium supplemented with keratin azure , the results revealed that 20 isolates appeared best ability to keratin analysis and nine isolates had best ability for keratinase production in submerged culture. According to this results T. mantagrophytes  (K3) (had  higher activity for  keratinase) was chosen for  molecular identification. The results of PCR revealed that primer for18S rRNA gene of T. mentagrophytes K1 isolate and specific primer for subtilisin like protease gene were amplified  and appeared as  single DNA band with a molecular base of   690 bp and 623bp respectively .The blast result of sample sequences of amplified fragment revealed that the  isolate were 100% identical to reference sequence of T.mentagrophytes var. interdigtal and depending on  data base in NCBI The result  of PCR product for enzyme showed new type named GBF60362 (402)   subtilisin-like protease  related to T. mentagrophytes 1354684064 BFBSOLP00892.


2019 ◽  
Vol 7 (1) ◽  
pp. 43
Author(s):  
Nery Sofiyanti ◽  
Mayta Novaliza Isda

Moss club (Lycopodiella cernua) is one of fern members distributed in Riau Province. The aimed of this study were to characterized the morphological characters and to analized its DNA sequence based on rbcl primer. Samples were collected from the field, documented and characterized the morphological charaters. DNA were isolated and amplified using PCR method and rbcl primer.  DNA sequnces were then analized using BLAST   Lycopodiella cernua collected from Riau Province was characterized by having creeping and erect rhizome that covered by microphyl, and terminal strobili. Rbcl fragmen of Lycopodiella cernua was sucssesfully amplified with 643 bp length. BLAST result confirmed the  rbcl fragmen of this club moss.


2017 ◽  
Vol 18 (4) ◽  
pp. 1358-1366
Author(s):  
MOHD LUTFI ABDULLAH ◽  
SITI AZIZAH MOHD NOR ◽  
DARLINA MD. NAIM

Abdullah ML, Nor SAM, Naim DMd. 2017. Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia. Biodiversitas 18: 1358-1366. The genus Ariidae contains many valuable fish species threatened by overfishing, but knowledge on distribution and threats is still limited due to taxonomic ambiguities. The aim of this study was to apply DNA barcoding techniques to establish a resource of DNA for identification of Ariidae species in Malaysia. A 621 bp of mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to resolve phylogenetic relationships and molecular taxonomy of eight presumed Malaysian Ariid species. We found the monophyly of most species was well established with a mean Kimura-2 parameter (K2P) interspecies distance of 9.6% except for two species, Arius venosus, and Nemapteryx caelata that have very low interspecies genetic distance. The BLAST result shows only two species matched the presumably eight identified fish species. Such discrepancies could arise as a result of misidentifications or errors in GenBank database input, hybridization or incomplete lineage sorting. We suggest the use of DNA barcoding is integrated into the workflow during taxonomic studies as it could significantly increase knowledge about species distributions.


2006 ◽  
Vol 3 (3) ◽  
pp. 237-242 ◽  
Author(s):  
Lin Fan-Yun ◽  
Hu Yin-Gang ◽  
Song Guo-Qi ◽  
Zhang Hong ◽  
Liu Tian-Ming ◽  
...  

AbstractIn order to investigate the molecular mechanism of rehydration after serious drought in broomcorn millet (Panicum miliaceum L.), a forward subtracted cDNA library was constructed between normal watered leaves and rehydrated leaves after serious drought conditions, using the suppressive subtraction hybridization (SSH) technique. A total of 60 positive clones were picked out at random from the subtracted library and sequenced, and redundancy sequences were removed after sequence alignment. Based on the results of sequence homologous comparison and function querying, 32 expressed sequence tags (EST) were highly homologous with known ESTs. Most of those sequences were related to either abiotic or biotic stress in plants. Of those sequences, 11 ESTs were homologous with ESTs in rat (Rattus norvegicus) liver after partial hepatectomy. The Blast result of proteins revealed that 28 ESTs were similar to known proteins. The functions of these proteins mainly involve signal transduction, transcription and protein processing. This experiment demonstrated that a range of specific genes was induced and expressed in broomcorn millet during the rehydration stage after serious drought.


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