Biomedical subjects

Jon K Laerdahl

Publications and source records attributed to Jon K Laerdahl.

6 recordsLinked to original sources

PubMed2006

preAssemble: a tool for automatic sequencer trace data processing.

BACKGROUND: Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. RESULTS: The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. CONCLUSION: preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Algorithms↗

PubMed2005

An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar).

BACKGROUND: The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physiological, morphological and behavioural changes to prepare the salmon for its new environment. These changes are called the parr-smolt transformation or smoltification, and pre-adapt the salmon for survival and growth in the marine environment. The development of hypo-osmotic regulatory ability plays an important part in facilitating the transition from rivers to the sea. The physiological mechanisms behind the developmental changes are largely unknown. An understanding of the transformation process will be vital to the future of the aquaculture industry. A knowledge of which genes are expressed prior to the smoltification process is an important basis for further studies. RESULTS: In all, 2974 unique sequences, consisting of 779 contigs and 2195 singlets, were generated for Atlantic salmon from two cDNA libraries constructed from the gills and the intestine, accession numbers [Genbank: CK877169-CK879929, CK884015-CK886537 and CN181112-CN181464]. Nearly 50% of the sequences were assigned putative functions because they showed similarity to known genes, mostly from other species, in one or more of the databases used. The Swiss-Prot database returned significant hits for 1005 sequences. These could be assigned predicted gene products, and 967 were annotated using Gene Ontology (GO) terms for molecular function, biological process and/or cellular component, employing an annotation transfer procedure. CONCLUSION: This paper describes the construction of two cDNA libraries from pre-smolt Atlantic salmon (Salmo salar) and the subsequent EST sequencing, clustering and assigning of putative function to 1005 genes expressed in the gills and/or intestine.

Animals↗

PubMed2005

Nucleophilic identity substitution reactions. The reaction between hydrogen fluoride and protonated alkyl fluorides.

The gas phase reactions between HF and the protonated alkyl fluorides MeFH+, EtFH+, Pr(i)FH+, and Bu(t)FH+ have been studied using ab initio methods. The potential energy profiles for both nucleophilic substitution (S(N)2) and elimination (E2) pathways have been investigated. Both backside Walden inversion and frontside nucleophilic substitution reaction profiles have been generated. Backside substitution is very favourable, but shows relatively little variation with the alkyl group. Frontside substitution reaction barriers are only slightly higher than the barrier for backside substitution for HF + MeFH+, and the difference in barrier heights for frontside and backside displacement seems negligible for the larger alkyl groups. Reaction barrier trends have been analysed and compared with the results of similar studies of the H2O/ROH2+ and NH3/RNH3+ systems (R = Me, Et, Pr(i), and Bu(t)). Compared to the two other classes, protonated fluorides have extreme structures which, with the exception of the Me substrate, are weakly bound complexes between an alkyl cation and HF. The results nourish the idea that nucleophilic substitution reactions are better understood in view of competition between frontside and backside substitution than from the traditional S(N)1/S(N)2 perspective.

Chemistry, Organic↗

PubMed2005

PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology.

PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith-Waterman and ParAlign. The ParAlign algorithm is similar to Smith-Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known as multimedia technology that is available in modern processors, but rarely used by other bioinformatics software, has been exploited to achieve the high speed. The software is also designed to run efficiently on computer clusters using the message-passing interface standard. A public search service powered by a large computer cluster has been set-up and is freely available at www.paralign.org, where the major public databases can be searched. The software can also be downloaded free of charge for academic use.

Algorithms↗

PubMed2003

Nucleophilic identity substitution reactions. The reaction between water and protonated alcohols.

The potential energy surfaces for the reaction between H2O and the protonated alcohols MeOH2+, EtOH2+, PriOH2+, and Bu(t)OH2+ have been explored by means of high level ab initio theoretical methods. Both nucleophilic substitution (SN2) and elimination (E2) pathways have been investigated. Front side (SNF) and the familiar back side (SNB) Walden inversion attack of the nucleophile have been found to be competing for the H2O Bu(t)OH2+ system. In contradiction with the customary relationship between so-called "steric effects" and barrier heights--more alkyl-substituted SN2 reaction centres have higher SN2 reaction barriers--the SN2 reaction barriers are found to be Et > Me > Pri > Bui. This result is in excellent agreement with available experimental data.

Journal Article↗

PubMed2003

Nucleophilic identity substitution reactions. The reaction between ammonia and protonated amines.

The gas phase reactions between NH3 and the protonated amines MeNH3+, EtNH3+, PriNH3+, and Bu(t)nH3+ have been studied by high level ab initio methods. Mass spectrometric experiments yielded no significant reaction products; this result being consistent with the calculated reaction barriers. The potential energy profiles for both nucleophilic substitution (SN2) and elimination (E2) pathways have been investigated. Both back side Walden inversion (SNB) and front side (SNF) nucleophilic reaction profiles have been generated. The SNB reaction barriers are found to be higher for the more alkyl substituted reaction centres. Reaction barrier trends have been analysed and compared with the results of a similar study of the H2O-ROH2+ system (R = Me, Et, Pri, and Bu(t)).

Journal Article↗