An algorithm to find similar internal sequence repeats

In recent years, identification of sequence patterns has been given immense importance to understand better their significance with respect to genomic organization and evolutionary processes. To this end, an algorithm has been derived to identify all similar sequence repeats present in a protein sequence. The proposed algorithm is useful to correlate the three-dimensional structure of various similar sequence repeats available in the Protein Data Bank against the same sequence repeats present in other databases like SWISS-PROT, PIR and Genome databases

weekly meeting

Proteins containing amino acid repeats are considered to be of great importance in evolutionary studies. The principal mechanism of formation of amino acid repeats is by the duplication or recombination of genes. Thus, repeats are found in both nucleotide and protein sequences. In proteins, repeats are involved in protein-protein interactions as well as in binding to other ligands such as DNA and RNA. The study of internal sequence repeats would be helpful to scientists in various fields, including structural biology, enzymology, phylogenetics, genomics and proteomics. Hence an algorithm (Finding All Internal Repeats, FAIR) has been designed utilizing the concepts of dynamic programing to identify the repeats. The proposed algorithm is a faster and more efficient method to detect internal sequence repeats in both protein and nucleotide sequences, than those found in the literature. The algorithm has been implemented in $C^{++}$ and a web-based computing engine, IdentSeek, has been developed to make FAIR accessible to the scientific community. IdentSeek produces a clear, detailed result (including the location of the repeat in the sequence and its length), which can be accessed through the world wide web at the URL http://bioserver1.physics.iisc.ernet.in/ident/

An algorithm to find similar internal sequence repeats

In recent years, identification of sequence patterns has been given immense importance to understand better their significance with respect to genomic organization and evolutionary processes. To this end, an algorithm has been derived to identify all similar sequence repeats present in a protein sequence. The proposed algorithm is useful to correlate the three-dimensional structure of various similar sequence repeats available in the Protein Data Bank against the same sequence repeats present in other databases like SWISS-PROT, PIR and Genome databases

Prenatal diagnosis and prevalence of critical congenital heart defects: an international retrospective cohort study

OBJECTIVES: To assess international trends and patterns of prenatal diagnosis of critical congenital heart defects (CCHDs) and their relation to total and live birth CCHD prevalence and mortality. SETTING: Fifteen birth defect surveillance programmes that participate in the International Clearinghouse for Birth Defects Surveillance and Research from 12 countries in Europe, North and South America and Asia. PARTICIPANTS: Live births, stillbirths and elective terminations of pregnancy for fetal anomaly diagnosed with 1 of 12 selected CCHD, ascertained by the 15 programmes for delivery years 2000 to 2014. RESULTS: 18 243 CCHD cases were reported among 8 847 081 births. The median total prevalence was 19.1 per 10 000 births but varied threefold between programmes from 10.1 to 31.0 per 10 000. CCHD were prenatally detected for at least 50% of the cases in one-third of the programmes. However, prenatal detection varied from 13% in Slovak Republic to 87% in some areas in France. Prenatal detection was consistently high for hypoplastic left heart syndrome (64% overall) and was lowest for total anomalous pulmonary venous return (28% overall). Surveillance programmes in countries that do not legally permit terminations of pregnancy tended to have higher live birth prevalence of CCHD. Most programmes showed an increasing trend in prenatally diagnosed CCHD cases. DISCUSSION AND CONCLUSIONS: Prenatal detection already accounts for 50% or more of CCHD detected in many programmes and is increasing. Local policies and access likely account for the wide variability of reported occurrence and prenatal diagnosis. Detection rates are high especially for CCHD that are more easily diagnosed on a standard obstetric four-chamber ultrasound or for fetuses that have extracardiac anomalies. These ongoing trends in prenatal diagnosis, potentially in combination with newborn pulse oximetry, are likely to modify the epidemiology and clinical outcomes of CCHD in the near future