Research article
Genomic analysis of expressed sequence tags in American black bear Ursus americanus
- † Equal contributors
1 CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
2 Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
3 Current address: Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, N-0316 Oslo, Norway
BMC Genomics 2010, 11:201 doi:10.1186/1471-2164-11-201
Published: 26 March 2010Additional files
Additional file 1:
Figure S1. Distribution of bear EST lengths.
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Additional file 2:
Figure S2. Distribution of sequence identities of bear EST to dog genome alignments.
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Additional file 3:
Figure S3. Distribution of log2-transformed EST numbers per unique cluster.
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Additional file 4:
Figure S4. Phylogenetic trees of four mammalian species estimated by maximum likelihood method
under GTR substitution model based upon the concatenated CDS regions from nuclear
genes (A) and mitochondrial genes (B). Numbers below the branch are bootstrap supporting
ratios and numbers above the branch are the average substitution numbers per site,
which are related to Ka and Ks by 
where Na and Ns are numbers of non-synonymous and synonymous sites.
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Additional file 5:
Table S1. The complete list of 154 bear genes showing rapid evolution in bear lineage.
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This file can be viewed with: Microsoft Excel Viewer
Additional file 6:
Figure S5. Multiple sequence alignments of full-length CSRP3 CDS nucleotide sequences in nine species. The LIM1 zinc-binding domain is marked with grey and the 60th site is highlighted in blue. The corresponding protein sequence alignment is shown in Figure 5A.
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