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Estimating the Homology to Somatic Genome and Repeat Content.

AT Anna A. Torgasheva
LM Lyubov P. Malinovskaya
KZ Kira S. Zadesenets
TK Tatyana V. Karamysheva
EK Elena A. Kizilova
EA Ekaterina A. Akberdina
IP Inna E. Pristyazhnyuk
ES Elena P. Shnaider
VV Valeria A. Volodkina
AS Alsu F. Saifitdinova
SG Svetlana A. Galkina
DL Denis M. Larkin
NR Nikolai B. Rubtsov
PB Pavel M. Borodin
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Reads from the zebra finch, Bengalese finch, Eurasian siskin, and pale martin GRC sequences were aligned to the assembly of the zebra finch genome (Taeniopygia_guttata-3.2.4) using BLAT (21). A custom python script was used to estimate the coverage of the zebra finch genome in 10-kb windows. Overlapping of regions with high coverage with zebra finch Ensembl gene predictions and nonzebra finch RefSeq (23) genes was revealed with the Ensembl genome browser. Repeat content of the GRC libraries and the zebra finch genome was assessed with RepeatMasker (25) by using the avian RepBase database (26).

Copyright and License information:  ©2019-04-29
Published under the PNAS license.

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