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The first mitochondrial genome of the firefly genus Inflata Boontop, Inflata indica (Lampyridae, Luciolinae) is reported here. Thirteen protein coding genes, 22 tRNA, 2 rRNA genes and a 1570 bp non-coding region were annotated. The comparative analysis showed that the size, GC content, gene content and gene arrangement of this mitochondrial genome are similar to those of other Lampyridae. The mitochondrial phylogenomic analysis showed that I. indica is clustered with other fireflies belonging to the subfamily Luciolinae and most closely related to Pteroptyx maipo. The evolutionary relationship within group of Luciolinae fireflies presented by complete COI phylogeny differs from the relationship based on the mitochondrial phylogenomic tree. This individual firefly also carries mitochondrial DNA (mtDNA) heteroplasmy; however, no potential effect of heteroplasmic mutations could be observed in this study. Hence, this study is reporting not only the first mitochondrial genome of the genus Inflata and the comparative mitochondrial genome analysis of fireflies but also the first mitochondrial DNA heteroplasmy in Lampyridae.
Pubmed ID: 30339996
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Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsSoftware for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.
View all literature mentionsCollection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
View all literature mentionsJava toolset for working with next generation sequencing data in the BAM format.
View all literature mentionsBiopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. It works along with the Open Bioinformatics Foundation, who generously host it''s website, bug tracker, and mailing lists. Sponsor: This resource is supported by the Open Bioinformatics Foundation. Keywords: Tool, Software, Python, Biological, Computation, Bioinformatics,
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software as system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsSoftware that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.
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