title: ApicoAlign: an alignment and sequence search tool for apicomplexan proteins.
abstract: BACKGROUND
  Over the recent years, a number of genomes have been successfully sequenced and this was followed by genome annotation projects to help understand the biological capabilities of newly sequenced genomes. To improve the annotation of Plasmodium falciparum proteins, we earlier developed parasite specific matrices (PfSSM) and demonstrated their (Smat80 and PfFSmat60) better performance over standard matrices (BLOSUM and PAM). Here we extend that study to nine apicomplexan species other than P. falciparum and develop a web application ApicoAlign for improving the annotation of apicomplexan proteins.
  
  
  RESULTS
  The SMAT80 and PfFSmat60 matrices perform better for apicomplexan proteins compared to BLOSUM in detecting the orthologs and improving the alignment of these proteins with their potential orthologs respectively. Database searches against non-redundant (nr) database have shown that SMAT80 gives superior performance compared to BLOSUM series in terms of E-values, bit scores, percent identity, alignment length and mismatches for most of the apicomplexan proteins studied here. Using these matrices, we were able to find orthologs for rhomboid proteases of P. berghei, P. falciparum & P. vivax and large subunit of U2 snRNP auxiliary factor of Cryptosporidium parvum in Arabidopsis thaliana. We also show improved pairwise alignments of proteins from Apicomplexa viz. Cryptosporidium parvum and P. falciparum with their orthologs from other species using the PfFSmat60 matrix.
  
  
  CONCLUSIONS
  The SMAT80 and PfFSmat60 substitution matrices perform better for apicomplexan proteins compared to BLOSUM series. Since they can be helpful in improving the annotation of apicomplexan genomes and their functional characterization, we have developed a web server ApicoAlign for finding orthologs and aligning apicomplexan proteins.
authors.affiliation: Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, A Sun Centre of Excellence in Medical Bioinformatics, Hyderabad 500001, India.
authors.forename: Jamshaid
authors.initials: J
authors.lastname: Ali
authors.forename: Umadevi
authors.initials: U
authors.lastname: Paila
authors.forename: Akash
authors.initials: A
authors.lastname: Ranjan
mesh_terms: D016782:Apicomplexa / Q000235:genetics* / Q000378:metabolism*; D016785:Cryptosporidium parvum / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D020407:Internet; D010963:Plasmodium falciparum / Q000235:genetics / Q000378:metabolism; D015800:Protozoan Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D057386:Search Engine; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D015800:Protozoan Proteins