https://www.cs.princeton.edu/~bee/courses/read/burge-jmb-1997.pdf

Prediction of Complete Gene Structures in Human Genomic DNA

https://www.cell.com/cell/pdf/S0092-8674(00)81965-0.pdf

The Sleep Disorder Canine Narcolepsy Is Caused by a Mutation in the Hypocretin (Orexin) Receptor 2 Gene

Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.

/pdf/complementary-dna-sequencing-expressed-sequence-tags-and-21r7ogldx5.pdf

Complementary DNA sequencing : expressed sequence tags and human genome project

Primary structure of the Aequorea victoria green-fluorescent protein.

Thousands of mutations are identified yearly. Although many directly affect protein expression, an increasing proportion of mutations is now believed to influence mRNA splicing. They mostly affect existing splice sites, but synonymous, non-synonymous or nonsense mutations can also create or disrupt splice sites or auxiliary cis-splicing sequences. To facilitate the analysis of the different mutations, we designed Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. It contains all available matrices for auxiliary sequence prediction as well as new ones for binding sites of the 9G8 and Tra2-beta Serine-Arginine proteins and the hnRNP A1 ribonucleoprotein. We also developed new Position Weight Matrices to assess the strength of 5' and 3' splice sites and branch points. We evaluated HSF efficiency using a set of 83 intronic and 35 exonic mutations known to result in splicing defects. We showed that the mutation effect was correctly predicted in almost all cases. HSF could thus represent a valuable resource for research, diagnostic and therapeutic (e.g. therapeutic exon skipping) purposes as well as for global studies, such as the GEN2PHEN European Project or the Human Variome Project.

https://www.hal.inserm.fr/inserm-00396239/document

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

A systematic analysis of the RNA splice junction sequences of eukaryotic protein coding genes was carried out using the GENBANK databank. Nucleotide frequencies obtained for the highly conserved regions around the splice sites for different categories of organisms closely agree with each other. A striking similarity among the rare splice junctions which do not contain AG at the 3' splice site or GT at the 5' splice site indicates the existence of special mechanisms to recognize them, and that these unique signals may be involved in crucial gene-regulation events and in differentiation. A method was developed to predict potential exons in a bare sequence, using a scoring and ranking scheme based on nucleotide weight tables. This method was used to find a majority of the exons in selected known genes, and also predicted potential new exons which may be used in alternative splicing situations.

RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression.

Publisher Summary There exists a sequence of 8 nucleotides, highly conserved at the boundary between an exon and an intron, referred to as the 5′ splice site (5′ ss). The boundary between an intron and an exon, the 3′ splice site (3′ ss), also exhibits a highly conserved sequence of 4 nucleotides, preceded by a pyrimidine-rich region. To interpret the deluge of sequence information generated by the human genome project, it is important to be able to identify genes in uncharacterized sequences. Without this capability, the sequence information is of little value. For each sequence in GenBank, the splice sites were located using the information in the annotation preceding the sequence, a FEATURES line being followed by multiple lines indicating different features present in the gene. The percentages of lariat windows with high-scoring branch point sequences in all GenBank categories, with the exception of viruses, are higher than those of random sequences. A notable observation is that even the window that contains the second highest frequency of branch points among the five windows analyzed always had a lower frequency of high scoring branch points than expected for a window with a random sequence.

Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project.

Replication of adeno-associated virus DNA. Complementation of naturally occurring rep- mutants by a wild-type genome or an ori- mutant and correction of terminal palindrome deletions.

Disclosed is a method for sequencing and amplifying nucleic acid templates wherein a degenerate primer with a fixed sequence region and a random sequence region is utilized. By determining the statistical expectancy of the fixed sequence in the nucleic acid template, this determines the average length of a nucleic acid template that can be sequenced. During the annealing of such a primer with the nucleic acid template, the fixed sequence determines where the complete primer binds by binding to its complementary sequence on the nucleic acid template. The random sequence regions of the primers make it possible for the presence of a unique sequence adjacent to the fixed sequence to be present, thus providing a primer with full complementarity with the nucleic acid template. Thus, this procedure is able to provide a full-length primer with a fully complementary sequence capable of binding statistically once within an expected length of the nucleic acid template, even though the seance of the template is unknown. The method can also be adopted for use in PCR amplification of a nucleic acid template.

Shot-gun sequencing and amplification without cloning

http://www.jbc.org/content/259/7/4661.full.pdf

Periannan Senapathy

Papers

RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression.

Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project.

Replication of adeno-associated virus DNA. Complementation of naturally occurring rep- mutants by a wild-type genome or an ori- mutant and correction of terminal palindrome deletions.

Shot-gun sequencing and amplification without cloning

Molecular cloning of adeno-associated virus variant genomes and generation of infectious virus by recombination in mammalian cells.