SPLICE, a computer program for automated extraction of information from GenBank sequence entries

SPLICE, a software tool for the extraction of sequences fromfiles in GenBank tape format, has been developed. The programcan analyze the features table in this format and use any ofthe information provided to write the corresponding sequencesinto a standard sequence file format suitable for use with sequenceanalysis programs. Sequences that are present as several subsequentfragments in a single GenBank file, such as those encoding apeptide, can be spliced together by the program. Further, sequencesthat are present in more than one Genbank file, such as an exonwhich spans several different files, can also be spliced intoone sequence. SPLICE runs under the MS/DOS and Unix operatingsystems, can be called as a sub-process by other programs andcan process batches of files. Received on December 26, 1989; accepted on May 30, 1990     

Methanogenic potential of Arctic and Antarctic subglacial environments with contrasting organic carbon sources

Subglacial environments are largely anoxic, contain organic carbon (OC) overridden by glacier ice during periods of advance, and harbour active microbial communities. This creates favourable conditions for OC degradation via methanogenesis. It has been hypothesized that OC beneath ice sheets is converted to methane (CH₄) and may be released to the atmosphere during retreat. However, there are limited data available to support this contention. Here, we present new data on the abundance, diversity and activity of methanogenic archaea and the amount and character of OC in subglacial sediments from Arctic and Antarctic glacial systems based on different substrate types. We employed long‐term laboratory incubations to quantify the CH₄ production potential in different subglacial settings. Significant numbers of methanogens (up to 7 × 10⁴ cells g^?1) were detected in the samples and clones of Methanomicrobiales and Methanosarcinales were identified in clone libraries. Long lag periods (up to >200 days) were observed before significant CH₄ concentrations were measured. We report order of magnitude differences in rates of CH₄ production (10¹–10⁵ fmol g^?1 d^?1) in different subglacial sediments, reflecting contrasts in the origin of the sediment and the OC character. Hence, we predict that contrasting rates of CH₄ production are likely to occur beneath glaciers and ice sheets that overran different types of substrate. We subsequently estimated the potential for CH₄ production beneath the Laurentide/Inuitian/Cordilleran and Fennoscandian Ice Sheets during a typical 85 ka Quaternary glacial/interglacial cycle. CH₄ production from lacustrine‐derived OC is likely to be an order of magnitude higher (~6.3–27 Pg C) than that from overridden soils (~0.55–0.68 Pg C), possibly due to a difference in lability between lacustrine and soil OC. While representing a fraction of the entire OC pool (~418–610 Pg C), this finding highlights the importance of considering the character of different OC pools when calculating subglacial CH₄ production.     

Mixed oligo designer (MOD), a computer program to aid planning of automated, mixed oligodeoxyribonucleotide synthesis for mutagenesis experiments

A computer program, MOD (mixed oligo designer), which aids in planning site-directed mutagenesis experiments using highly substituted oligodeoxyribonucleotides (oligos), is described. The program calculates the relationship between the degree of oligo substitution and the mutation frequency, in order to achieve an optimal level of mutagenesis. The program can be used on a wide variety of computers and runs under a number of different operating systems.     

Relationships among DNA sequences of the 1.3 kb EcoRI family of mouse DNA

Summary The genome of the mouse (Mus musculus) contains a family of repeated DNA sequences defined by a 1.3 kb EcoRI fragment. Resqtriction maps of ten cloned fragments from this family have been determined. The fragments were of seven different types, based on the patterns of digestion obtained with AvaII, HindIII, and TaqI restriction enzymes. These seven unique sets of sequences fell into two classes, as defined by the position of a single HindIII site. Portions of fragments from each of the two classes were sequenced. Although certain regions of the repeat were highly conserved between classes, there was more intraspecific sequence divergence among the sequenced regions than has been observed for the short interspersedAlu family of repeated sequences sin mammals. Sequences of both HindIII classes were found to be present within the mouse X chromosome; we can conclude that both classes must also be present on other mouse chromosomes.     

BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability

We have written a computer program, BIGPROBE, which facilitates the design of long nucleic acid probes from the partial or complete amino acid sequence of a protein. BIGPROBE relies upon information on codon usage, intercodon dinucleotide frequency, and potential probe self-complementarity. We have examined the accuracy with which the program predicts coding sequences using sample human and rat genes and probe lengths of 30-60 nucleotides. Rat probe sequences selected by BIGPROBE using either codon usage or dinucleotide frequency data alone averaged 86-92% homology with the known exons of the corresponding gene sequences. Predictive accuracy with rat gene probes could be improved to 89-94%, depending upon probe length, by applying codon usage and dinucleotide frequency data in combination. Similar accuracy was achieved for human genes.