@article {310506,
	title = {Human-specific insertions and deletions inferred from mammalian genome sequences.},
	journal = {Genome Res},
	volume = {17},
	year = {2007},
	month = {01/2007},
	pages = {16-22},
	abstract = {<p>It has been suggested that insertions and deletions (indels) have contributed to the sequence divergence between the human and chimpanzee genomes more than do nucleotide changes (3\% vs. 1.2\%). However, although there have been studies of large indels between the two genomes, no systematic analysis of small indels (i.e., indels <!--= 100 bp) has been published. In this study, we first estimated that the false-positive rate of small indels inferred from human-chimpanzee pairwise sequence alignments is quite high, suggesting that the chimpanzee genome draft is not sufficiently accurate for our purpose. We have therefore inferred only human-specific indels using multiple sequence alignments of mammalian genomes. We identified -->840,000 "small" indels, which affect \&gt;7000 UCSC-annotated human genes (\&gt;11,000 transcripts). These indels, however, amount to only approximately 0.21\% sequence change in the human lineage for the regions compared, whereas in pseudogenes indels contribute to a sequence divergence of 1.40\%, suggesting that most of the indels that occurred in genic regions have been eliminated. Functional analysis reveals that the genes whose coding exons have been affected by human-specific indels are enriched in transcription and translation regulatory activities but are underrepresented in catalytic and transporter activities, cellular and physiological processes, and extracellular region/matrix. This functional bias suggests that human-specific indels might have contributed to human unique traits by causing changes at the RNA and protein level.</p>
},
	keywords = {Animals, Base Sequence, Chromosomes, Human, Pair 21, Evolution, Molecular, Gene Deletion, Genes, Regulator, Genome, Genome, Human, Humans, Mammals, Molecular Sequence Data, Mutagenesis, Insertional, Pan troglodytes, Protein Biosynthesis, Sequence Alignment, Transcription, Genetic},
	issn = {1088-9051},
	doi = {10.1101/gr.5429606},
	author = {Chen, Feng-Chi and Chen, Chueng-Jong and Li, Wen-Hsiung and Chuang, Trees-Juen}
}
