alignments of target protein sequences
收藏DataONE2015-03-20 更新2024-06-27 收录
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The target gene open reading frame protein sequences (MHC, TLR, RLR, KoRV) from the Trinotate analysis were first aligned with eutherian, marsupial, and other vertebrate sequences using Jalview 2.8.0b1 and MUSCLE using default parameters. An intital neighbor joining tree was created (using MEGA 5.2.2) and used to guide the alignments of each individual gene clade via Jalview and MUSCLE (with the exception of MHC sequences which were aligned using HMMER 3.1b and PFAM seed alignments). These gene group alignments were then combined using COACH (version 11/21/2002 Linux) and additional sequences were added as needed. The ends of the alignments were trimmed, when necessary, and both the full and trimmed alignments (.fas format) are included in this file package. For more detailed methods please refer to the associated publication.
创建时间：
2015-03-20
