A method for clustering of miRNA sequences using fragmented programming.

Clustering of miRNA sequences is an important problem in molecular genetics associated cellular biology. Thousands of such sequences are known today through advancement in sophisticated molecular tools, sequencing techniques, computational resources and rule based mathematical models. Analysis of such large-scale miRNA sequences for inferring patterns towards deducing cellular function is a great challenge in modern molecular biology.

miR-1322 Binding Sites in Paralogous and Orthologous Genes.

We searched for 2,563 microRNA (miRNA) binding sites in 17,494 mRNA sequences of human genes. miR-1322 has more than 2,000 binding sites in 1,058 genes with ΔG/ΔG m ratio of 85% and more. miR-1322 has 1,889 binding sites in CDSs, 215 binding sites in 5' UTRs, and 160 binding sites in 3' UTRs.

miRAFinder and GeneAFinder scripts: large-scale searching for miRNA and related information in indexed literature abstracts.

Unlabelled: In recent times, information on miRNAs and their binding sites is gaining momentum. Therefore, there is interest in the development of tools extracting miRNA related information from known literature. Hence, we describe GeneAFinder and miRAFinder scripts (open source) developed using python programming for the semi-automatic extraction and arrangement of updated information on miRNAs, genes and additional data from published article abstracts in PubMed.

Binding sites of miR-1273 family on the mRNA of target genes.

This study examined binding sites of 2,578 miRNAs in the mRNAs of 12,175 human genes using the MirTarget program. It found that the miRNAs of miR-1273 family have between 33 and 1,074 mRNA target genes, with a free hybridization energy of 90% or more of its maximum value. The miR-1273 family consists of miR-1273a, miR-1273c, miR-1273d, miR-1273e, miR-1273f, miR-1273g-3p, miR-1273g-5p, miR-1273h-3p, and miR-1273h-5p.

TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues.

Unlabelled: microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences.

MiR-3960 binding sites with mRNA of human genes.

The importance of miRNA in cellular regulation is gaining momentum. Therefore, it is of interest to study miRNA in human genes. Hence, the humanmRNA sequences (12,175) were searched for miRNA binding sites and 2,563predicted sites were found.

The properties of binding sites of miR-619-5p, miR-5095, miR-5096, and miR-5585-3p in the mRNAs of human genes.

The binding of 2,578 human miRNAs with the mRNAs of 12,175 human genes was studied. It was established that miR-619-5p, miR-5095, miR-5096, and miR-5585-3p bind with high affinity to the mRNAs of the 1215, 832, 725, and 655 genes, respectively. These unique miRNAs have binding sites in the coding sequences and untranslated regions of mRNAs.

miRNA and tropism of human parvovirus B19.

Parvovirus B19 has an extreme tropism for human erythroid progenitors. Here we propose the hypothesis explaining the tropism of human parvovirus B19. Our speculations are based on experimental results related to the capsid proteins VP1 and VP2.

Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis.

miRNAs regulate gene expression by binding with mRNAs of many genes. Studying their effects on genes involved in oncogenesis is important in cancer diagnostics and therapeutics. The RNAHybrid 2.

Physiological change in camel milk composition (Camelus dromedarius) 1. Effect of lactation stage.

The change in the composition of camel milk in four dromedaries was studied by including the common measured parameters: protein, total fat, lactose, main minerals (calcium, phosphorus, and iron), and vitamin C. The fat matter varied from 4.34% to 7.

Using profiles based on nucleotide hydrophobicity to define essential regions for splicing.

The splice-site sequences of U2-type introns are highly degenerate, so many different sequences can function as U2-type splice sites. Using our new profiles based on hydrophobicity properties we pointed out specific properties for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes extracted from GenBank to define positions having conserved properties, namely hydrophobicity, that are potentially essential for recognition by spliceosome.