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LETTER: Low-Complexity Regions in Plasmodium falciparum Proteins
- Elisabetta Pizzi and
- Clara Frontali
Genome Res. February 1, 2001 11: 218-229; Published in Advance January 18, 2001, doi:10.1101/gr.152201
...Low-Complexity Regions in Plasmodium falciparum Proteins Elisabetta Pizzi and Clara Frontali 1 Laboratorio di Biologia Cellulare, Istituto Superiore di Sanitá, 00161 Rome, Italy Abstract Full-sequence data available for Plasmodium falciparum...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...structure searches, 1414 CDSs were further assessed for confidence, and 1008 predicted structures were assigned as high-confidence by random forest categorization. In CpIRef, 143 previously uncharacterized proteins were assigned high-confidence GO terms.New transporter genes are identifiedWe further...
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LETTER: Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
- Tobias Mourier,
- Celine Carret,
- Sue Kyes,
- Zoe Christodoulou,
- Paul P. Gardner,
- Daniel C. Jeffares,
- Robert Pinches,
- Bart Barrell,
- Matt Berriman,
- Sam Griffiths-Jones,
- Alasdair Ivens,
- Chris Newbold,
- and Arnab Pain
Genome Res. February 2008 18: 281-292; Published in Advance December 20, 2007, doi:10.1101/gr.6836108
...% of the . These sequences were searched for similarity against the other Plasmodium s using WU-BLASTN ( http://blast.wustl.edu/ ) with dust and seg low-complexity filters. Only hits with a length ≥50 bp and with at least 70% identity were further processed. BLAST-matches were mapped back at the P. falciparum and merged...
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LETTER: De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring
- Pontus Larsson,
- Andrea Hinas,
- David H. Ardell,
- Leif A. Kirsebom,
- Anders Virtanen,
- and Fredrik Söderbom
Genome Res. June 2008 18: 888-899; Published in Advance March 17, 2008, doi:10.1101/gr.069104.107
...RNA genes using a compositional contrast approach combined with a search for conserved regions among three closely related Plasmodium species ( Upadhyay et al. 2005 ). This study reported 18 candidates for new ncRNA genes, of which six could be detected by Northern blot analysis ( Upadhyay et al. 2005...
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LETTER: Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion
- Nuno L. Barbosa-Morais,
- Maria Carmo-Fonseca,
- and Samuel Aparício
Genome Res. January 2006 16: 66-77; Published in Advance December 12, 2005, doi:10.1101/gr.3936206
...of the likelihood of splice sites. This curation was assisted by BLAST, Wise 2, and EST searches, carried out in the Gene2EST BLAST Server ( Gemund et al. 2001 ) (EMBL, http://woody.embl-heidelberg.de/gene2est ) and the NCBI BLAST website ( http://www.ncbi.nlm.nih.gov/BLAST , blastn, low complexity filter on...
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LETTER: Functional insights from the distribution and role of homopeptide repeat-containing proteins
- Noel G. Faux,
- Stephen P. Bottomley,
- Arthur M. Lesk,
- James A. Irving,
- John R. Morrison,
- Maria Garcia de la Banda,
- and James C. Whisstock
Genome Res. April 2005 15: 537-551; doi:10.1101/gr.3096505
...cerevisiae, Plasmodium falciparum, Oryza sativa, Triticum aestivum , and Arabidopsis thaliana . The longest sequence from each of the prokaryote clusters was used as probes to search GENPEPT using PSI-BLAST. The following parameters were used: j = 5, b = 100,000, e = 0.001, and -F T. All sequences...
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Method: Detection of simple and complex de novo mutations with multiple reference sequences
- Kiran V. Garimella,
- Zamin Iqbal,
- Michael A. Krause,
- Susana Campino,
- Mihir Kekre,
- Eleanor Drury,
- Dominic Kwiatkowski,
- Juliana M. Sá,
- Thomas E. Wellems,
- and Gil McVean
Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
...to simulating SNVs, MNVs/indels with random sequence, and inversions, special care was taken to simulate variants arising from repeat expansion and contraction by searching for existing repetitive regions in the and adding or subtracting repeat units. NAHR events were simulated by recombining members...
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Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
- Ulrike Böhme,
- Thomas D. Otto,
- James A. Cotton,
- Sascha Steinbiss,
- Mandy Sanders,
- Samuel O. Oyola,
- Antoine Nicot,
- Sylvain Gandon,
- Kailash P. Patra,
- Colin Herd,
- Ellen Bushell,
- Katarzyna K. Modrzynska,
- Oliver Billker,
- Joseph M. Vinetz,
- Ana Rivero,
- Chris I. Newbold,
- and Matthew Berriman
Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
...1 and SURFIN families, respectively. Next, we searched for those predicted motifs in all predicted proteins (excluding low-complexity regions) of the 11 sequenced Plasmodium species and visualized the results as a binary occurrence matrix (Supplemental Fig. S14B). Although some proteins share...
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LETTER: Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization
- King-Hwa Ling,
- Marie-Adele Rajandream,
- Pierre Rivailler,
- Alasdair Ivens,
- Soon-Joo Yap,
- Alda M.B.N. Madeira,
- Karen Mungall,
- Karen Billington,
- Wai-Yan Yee,
- Alan T. Bankier,
- Fionnadh Carroll,
- Alan M. Durham,
- Nicholas Peters,
- Shu-San Loo,
- Mohd Noor Mat Isa,
- Jeniffer Novaes,
- Michael Quail,
- Rozita Rosli,
- Mariana Nor Shamsudin,
- Tiago J.P. Sobreira,
- Adrian R. Tivey,
- Siew-Fun Wai,
- Sarah White,
- Xikun Wu,
- Arnaud Kerhornou,
- Damer Blake,
- Rahmah Mohamed,
- Martin Shirley,
- Arthur Gruber,
- Matthew Berriman,
- Fiona Tomley,
- Paul H. Dear,
- and Kiew-Lian Wan
Genome Res. March 2007 17: 311-319; Published in Advance February 6, 2007, doi:10.1101/gr.5823007
...with reference to Eimeria ESTs and to known genes in other apicomplexans. In the second, alignment of genomic sequence with Eimeria ESTs and BLAST searches of the Eimeria chromosomal sequence against proteins from other apicomplexans were used to find further genes not identified by the prediction tools...
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LETTER: Comparative Analysis of Apicomplexa and Genomic Diversity in Eukaryotes
- Thomas J. Templeton,
- Lakshminarayan M. Iyer,
- Vivek Anantharaman,
- Shinichiro Enomoto,
- Juan E. Abrahante,
- G.M. Subramanian,
- Stephen L. Hoffman,
- Mitchell S. Abrahamsen,
- and L. Aravind
Genome Res. September 2004 14: 1686-1695; doi:10.1101/gr.2615304
...complexity, proline- and valine-rich proteins called articulins ( Mann and Beckers 2001 ). We identified 10 distinct articulins in Plasmodium and six in Cryptosporidium having composition and sequence similarity to the articulins from other alveolates such as the ciliate, Pseudomicrothorax . This suggests...

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