More on manipulating text.

2021 ◽  
pp. 257-274
Author(s):  
Donald L. J. Quicke ◽  
Buntika A. Butcher ◽  
Rachel A. Kruft Welton
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
White Spaces ◽  
Using Data ◽  
Unknown Length

Abstract This chapter provides more information on manipulating text, presenting two examples. Example 1 focuses on standardizing names in a phylogenetic tree description, using R to reformat taxon names, create lists, sort data and use wildcards for when some things you are interested in don't have exactly the same length. The example tree description concerns parasitoids of caterpillars at a study site that have been DNA barcoded and their possible taxonomic identities added automatically. Example 2 deals with substrings of unknown length. This example search for a numeric substring of unknown length but with a standard prefix, using data of some DNA sequences from a set of Aleiodes wasps. The trimming of white spaces and/or tabs, use of wildcards to locate internal letter strings, finding of suffixes, prefixes and specifying of letters, numbers and punctuation, manipulation of character case, ignoring of character case, and specifying of particular and modifiable character classes are briefly described.

scholarly journals ЦАХИЛДАГНЫ ТӨРЛИЙН УРГАМЛЫН ФИЛОГЕНЕТИК ХОЛБОО

2016 ◽  
pp. 25-31
Author(s):  
Х Алтанзул ◽  
Ю Оюунбилэг
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Relationship ◽  
Dna Sequences ◽  
Fragment Size ◽  
Dna Fragment ◽  
Relationship Of

The phylogenetic relationship of eight Iris species (I.flavisimma, I.ventricosa, I.bungei,I.kaempferi, I.tenuifolia, I.lactea, I.tigrida, I.dichotoma) were studied by PCR using six specificprimers (S-523, Z1204R, trnL, trnF and ITS1, ITS4). All species except I.ventricosa wereidentified when using S-523, Z1204R and trnL, trnF primers and the DNA fragment size rangedbetween 500 to 600 bp and 800 bp, respectively. Primers ITS1 and ITS4 produced double bandsin about 500 and 1500 bp to I.bungei, I.kaempferi, and I.lactea species. On the phylogenetic tree, some iris species have close relations based on chloroplastic DNA sequences. The closest relationships showed between I.sanguinea and I.sibirica, I.rutenica and I.uniflora. Also I.tenuifolia, I.ventricosa and I.halophila located on one branch of phylogenetic tree.

scholarly journals Phylogenetic Tree Construction for DNA Sequences using Clustering Methods

2012 ◽  
Vol 38 ◽  
pp. 1362-1366 ◽  
Author(s):  
Gayatri Mahapatro ◽  
Debahuti Mishra ◽  
Kailash Shaw ◽  
Sashikala Mishra ◽  
Tanushree Jena
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Clustering Methods ◽  
Phylogenetic Tree Construction ◽  
Tree Construction

Reconstruction of Phylogenetic Tree for COX with DNA Sequences

2020 ◽  
pp. 369-375
Author(s):  
D. Anurag ◽  
Chukka Santhaiah ◽  
N. V. Krishna Rao ◽  
V. JaswanthSai ◽  
P. Akash ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences

Strelitziana sarbhoyi sp. nov. (Strelitzianaceae, Chaetothyriales), from North-Western Himalayas, India, described based on morphology and molecular phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 427 (1) ◽  
pp. 51-59
Author(s):  
SHIWALI RANA ◽  
SANJAY KUMAR SINGH ◽  
PARAS NATH SINGH
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Culture Collection ◽  
Fungal Culture ◽  
Western Himalayas ◽  
Holotype Specimen ◽  
North Western

Strelitziana sarbhoyi is established as a new species to accommodate a phylloplane fungus isolated from Mallotus philippensis collected from Kangra region of North-Western Himalayas, Himachal Pradesh. The identity of the fungus is confirmed based on the asexual-morphs, cultural characteristics and phylogenetic analyses of the internal transcribed spacer (ITS) rDNA and partial nuclear ribosomal 28S large subunit (LSU) sequence data. The placement of S. sarbhoyi in the phylogenetic tree was determined based on DNA sequences from authenticated isolates of Strelitziana. Strelitziana sarbhoyi shows nearly 94% similarity with other known species of Strelitziana. Area description is provided for the proposed taxon along with microscopic images, and a phylogenetic tree. This is probably the first report of Strelitziana from India. Holotype specimen (dried voucher culture) is deposited in the Ajrekar Mycological Herbarium (AMH), and an ex-type culture is deposited in National Fungal Culture Collection of India (NFCCI).

scholarly journals Proteomic similarity of the Littorinid snails in the evolutionary context

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8546 ◽  
Author(s):  
Arina L. Maltseva ◽  
Marina A. Varfolomeeva ◽  
Arseniy A. Lobov ◽  
Polina Tikanova ◽  
Marina Panova ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
Geographic Location ◽  
Body Part ◽  
Specific Protein ◽  
Protein Markers ◽  
Cophenetic Correlation ◽  
Additional Information ◽  
History Of ◽  
Using Data

Background The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. Methods Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering—using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson–Foulds distance, the Fowlkes–Mallows index and cophenetic correlation. Results Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups (“saxatilis” and “obtusata” groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.

scholarly journals Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

2019 ◽  
Vol 48 (4) ◽  
pp. 1099-1106
Author(s):  
Emre Sevindik ◽  
Zehra Tuğba Murathan ◽  
Sümeyye Filiz ◽  
Kübra Yalçin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nucleotide Composition ◽  
Neighbor Joining ◽  
Sequencing Data ◽  
F Region ◽  
Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

scholarly journals Filogenetik Human papillomavirus (HPV) tipe 6 dan tipe 11 pada penderita recurrent respiratory papillomatosis

2014 ◽  
Vol 44 (1) ◽  
pp. 52
Author(s):  
Lenny Buana Wuriningtyas ◽  
Dwi Reno Pawarti ◽  
Achmad Chusnu Romdhoni
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Arithmetic Mean ◽  
Recurrent Respiratory Papillomatosis ◽  
Open Reading Frame ◽  
Group Method ◽  
Cross Sectional ◽  
Reading Frame ◽  
Pair Group ◽  
Unweighted Pair Group Method

Latar belakang: Papiloma saluran pernapasan berulang (recurrent respiratory papillomatosis/RRP) merupakan neoplasma jinak laring terbanyak akibat infeksi HPV tipe 6 dan tipe 11. RRP merupakan masalah terkait agresivitas dan terapi. Analisis genetik digunakan untuk membedakan varian HPV tipe 6 dan tipe 11. Filogenetik mengevaluasi evolusi sequen DNA virus. Tujuan: Penelitian bertujuan mengidentifikasi sequen DNA dan menganalisis pohon filogenetik HPV tipe 6 dan tipe 11 pada papiloma saluran pernapasan berulang. Metode: Penelitian merupakan observasional deskriptif cross sectional. Analisis menggunakan data pembanding dari GenBank. Filogenetik disusun menggunakan metodeUPGMA (Unweighted Pair Group Method with Arithmetic Mean). Didapatkan 15 sampel jaringan papiloma. Dilakukan pemeriksaan PCR dan analisis sequen DNA. Hasil: Dari 15 sampel penelitian (12 laki-laki, 3 perempuan) didapatkan 9 isolat HPV tipe 6 (8 varian dan 1 subtipe) dan 4 isolat HPV tipe 11 (3 varian dan 1 subtipe). Terdapat mutasi titik yang mengakibatkan munculnya varian dan subtipe HPV tipe 6 maupun tipe 11. Kesimpulan: sequen DNA sampel berasal dari L1 ORF (Late 1 Open Reading Frame) yang merupakan kapsid mayor virus. Proses mutasi level gen berupa substitusi, insersi, dan delesi.Subtipe HPV tipe 6 dan tipe 11 yang ditemukan diperkirakan sebagai subtipe baru dan belum pernah dilaporkan sebelumnya. Lima varian HPV tipe 6 membentuk satu cabang tersendiri pada nomenklatur filogenetik yang sudah ada sehingga diajukan sebagai sublineage baru (sublineage C). Seluruh isolat HPV tipe 11 membentuk cabang pohon tersendiri dan diajukan sebagai sublineage baru (sublineage B).Kata kunci: HPV tipe 6 dan 11, variasi sequen DNA, pohon filogenetik HPV tipe 6 and 11. ABSTRACTBackground: Recurrent respiratory papillomatosis (RRP) is the most common laryngeal benign neoplasm caused by infection of HPV type 6 and 11. RRP is still a serious problem related to agresivity and therapy. Genetic analysis used to determine the variant of HPV type 6 or 11. Phylogenetic tree used to evaluate the evolution of viral DNA squence. Purpose: This study aimed to identify DNA squences and analyse the phylogenetic tree of HPV type 6 and 11 in RRP. Methods: this was a descriptive observational cross sectional study. Data analysis used GenBank database and phylogenetic tree was constructed usedUPGMA (Unweighted Pair Group Method with Arithmetic Mean). 15 papillomas biopsies from RRP patients subjected HPV typing using PCR dan DNA sequensing analysis. Result: From 15 patients with RRP (12 male, 3 female), there were 9 isolates HPV type 6 (8 variants, 1 subtype) and 4 isolates HPV type 11 (3 variants, 1 subtype). There was a point mutation in HPV type 6 and 11. Conclusion: L1 ORF (Late 1 Open Reading Frame) sequensials DNA samples was virus major capsid. There were mutational process at gene level (substitution, insertion, deletion). Subtype of HPV-6 and 11, might be new ones, and had not been reported yet. Five variants of HPV type 6 constructed a different lineage in phylogenetic and it is proposed to be C sublineage. All samples HPV type 11 proposed as B sublineage. Keywords: HPV type 6 and 11, DNA sequences variations, phylogenetic trees HPV type 6 and 11.

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