Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes

2006 ◽  
pp. 265-280 ◽  
Author(s):  
Sagi Snir ◽  
Lior Pachter
Keyword(s):  
Insertions And Deletions ◽  
Phylogenetic Profiling

scholarly journals Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions

2009 ◽  
Vol 19 (7) ◽  
pp. 1153-1164 ◽  
Author(s):  
E. M. Kvikstad ◽  
F. Chiaromonte ◽  
K. D. Makova
Keyword(s):  
Multiscale Analysis ◽  
Insertions And Deletions

scholarly journals Peculiar Evolutionary History of miR390-Guided TAS3-Like Genes in Land Plants

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Maria S. Krasnikova ◽  
Denis V. Goryunov ◽  
Alexey V. Troitsky ◽  
Andrey G. Solovyev ◽  
Lydmila V. Ozerova ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Physcomitrella Patens ◽  
Land Plant ◽  
Plant Evolution ◽  
Marchantia Polymorpha ◽  
History Of ◽  
Molecular Machinery ◽  
Specific Mrnas ◽  
Land Plant Evolution ◽  
Phylogenetic Profiling

PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant moss taxa, namely, classes Bryopsida, Tetraphidopsida, Polytrichopsida, Andreaeopsida, and Sphagnopsida. We found relatives of allPhyscomitrella patensmiR390 and TAS3-like loci in these plant taxa excluding Sphagnopsida. Importantly, cloning and sequencing ofMarchantia polymorphagenomic DNA showed miR390 and TAS3-like sequences which were also found among genomic reads ofM. polymorphaat NCBI database. Our data suggest that the ancient plant miR390-dependent TAS molecular machinery firstly evolved to target AP2-like mRNAs in Marchantiophyta and only then both ARF- and AP2-specific mRNAs in mosses. The presented analysis shows that moss TAS3 families may undergone losses of tasiAP2 sites during evolution toward ferns and seed plants. These data confirm that miR390-guided genes coding for ARF- and AP2-specific ta-siRNAs have been gradually changed during land plant evolution.

Plasmodium vivax merozoite surface protein PvMSP-3β is radically polymorphic through mutation and large insertions and deletions

2004 ◽  
Vol 4 (4) ◽  
pp. 309-319 ◽  
Author(s):  
Julian C. Rayner ◽  
Curtis S. Huber ◽  
Dmitry Feldman ◽  
Paul Ingravallo ◽  
Mary R. Galinski ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Insertions And Deletions

scholarly journals Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling

2013 ◽  
Vol 9 (1) ◽  
pp. 692 ◽  
Author(s):  
Yuval Tabach ◽  
Tamar Golan ◽  
Abrahan Hernández‐Hernández ◽  
Arielle R Messer ◽  
Tomoyuki Fukuda ◽  
...  
Keyword(s):  
Human Disease ◽  
Disease Locus ◽  
Molecular Pathways ◽  
Phylogenetic Profiling

Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks

2005 ◽  
Vol 18 (5-6) ◽  
pp. 835-842 ◽  
Author(s):  
Derong Liu ◽  
Xiaoxu Xiong ◽  
Zeng-Guang Hou ◽  
Bhaskar DasGupta
Keyword(s):  
Neural Networks ◽  
Protein Sequences ◽  
Insertions And Deletions ◽  
Self Organizing
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