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Comparative genomics : nematode specific indels

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[Sept.15.2015]   
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Nematode Specific InDels

Insertions and deletions (indels) are important sequence variants which are considered as phylogenetic markers that reflect evolutionary adaptations in different species. This is part of our recent work to identify nematode specific indels based on transcriptome data. We examined over 160,000 polypeptides from 10 nematode species (9 parasitic and 1 non-parasitic species), compared them to 5 non-nematodes and identified indels unique to nematode proteins in more than 5,000 protein families.



PUBLICATION

Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting.
Wang Q, Heizer E, Rosa BA, Wildman SA, Janetka JW, Mitreva M.   Infect Genet Evol.   2016 Apr;39:201-11

RESOURCES

These alignments and indel annotations are the basis of our downstream analysis, including functional classifications, composition analysis and structure locations.

Sequence data
Protein fasta sequence used to build orthologous groups via orthoMCL:

Nematodes
Ancylostoma ceylanicum Ascaris suum Brugia malayi
Caenorhabditis elegans Haemonchus contortus Loa loa
Trichuris muris Trichuris muris Trichinella spiralis
Trichuris suis    

References
Drosophila melanogaster Homo sapiens Ovis aries
Saccharomyces cerevisiae Sus scrofa  


Group-specific multiple alignments
Nematode orthologous group sequence mulitple alignments
fam.aligned.tar.gz

Reference orthologous group sequence mulitple alignments
ref.aligned.tar.gz

Orthologous group definition
InDel annotation based on orthologous groups

Orthologous group definition file Formatting:
For DELETIONS & SHARED:
#start | #end | #num seqs shared | #num seqs not shared | #num seqs no information | ids of sequences shared | ids of sequences not shared | ids of sequences have no information

For INSERTIONS:
#start | #end | #num refs (these are of the refs) | #start | #end | #num seqs shared | #num seqs not shared | #num seqs no information | ids of sequences shared | ids of sequences not shared | ids of sequences have no information


 
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