MOTIVATION The alignment of DNA sequences to proteins, allowing for frameshifts, is a classic method in sequence analysis. It can help identify pseudogenes (which accumulate mutations), analyze raw DNA and RNA sequence data (which may have frameshift sequencing errors), investigate ribosomal frameshifts, etc. Often, however, only ad hoc approximations or simulations are available to provide the...

The RNA polymerase of giardiavirus (GLV) is synthesized as a fusion protein through a -1 ribosomal frameshift in a region where gag and pol open reading frames (ORFs) overlap. A heptamer, CCCUUUA, and a potential pseudoknot found in the overlap were predicted to be required for the frameshift. A 68-nucleotide (nt) cDNA fragment containing these elements was inserted between the GLV 5' 631-nt cD...

Truncating mutations including frameshift mutations and nonsense mutations contribute to ~45% of all mutations leading to NF1. However, the extent to which specific mechanisms are involved in causing these mutations has not been well explored yet. Here, we analyzed the frequency and characteristics of 1,924 and 1,731 NF1 individuals carrying frameshift and nonsense mutations respectively out of...

Instability of repetitive sequences, both in intronic sequences and within coding regions, has been demonstrated to be a hallmark of genomic instability in human cancer. Understanding how these mutational events arise may provide an opportunity for prevention or early intervention in cancer development. To study the source of this instability, we have identified a region of the beta-lactamase g...

It has been suggested that somatic mutations that accumulate due to an age related decline in the efficiency of DNA repair mechanisms might contribute to the increased incidence of cancer in older people. However, there is little direct evidence for this phenomenon. The spectra of germline and somatic mutations can be compared in cancer genes that cause inherited tumour syndromes and sporadic t...

Abstract Retinal dystrophies associated to mutations in the CRB1 gene comprise a wide array of clinical presentations. A blood sample from patient with family history CRB1-retinal dystrophy was used prepare iPSC line ESi082-A. The genotype donor, affected perifoveal-bilateral macular includes one frameshift deletion and hypomorphic allele. ESi082-A cell has been characterized for pluripotency w...

We investigated the prognostic value of p53 mutation type for 145 soft tissue sarcoma patients. In a PCR-SSCP-sequencing analysis, 15 mutations were identified: 10 non-frameshift (non-fs) and 5 frameshift (fs) mutations. Patients possessing non-fs mutations had a significantly poorer prognosis than patients without p53 mutations (P = 0.014), according to Cox's multivariate analysis. In contrast...

We are interested in a sequence the more homogeneous as poss composition to compare its frequency with a less homogeneous one. First t codons composed by the repetition of the same nucleotide: AAA, CCC, GGG and TTT in Figure 1). If we look at the amino a acids that are associated also with frequency of 2 sequences undergoing differences due to the fact that the associated amino acids could be c...

Mononucleotide repeat sequences are particularly prone to frameshift mutations in tumors with biallelic inactivation of the mismatch repair (MMR) genes MLH1 or MSH2. In these tumors, several genes harboring mononucleotide repeats in their coding region have been proposed as targets involved in tumor progression, among which are also the MMR genes MSH3 and MSH6. We have analyzed the expression o...