Protocols
- A Guide to Molecular Sequence Analysis (Andrew S. Louka , www.SequenceAnalysis.com)
This guide will introduce the reader to molecular sequence analysis. In the context of this guide, sequence analysis is the process of trying to find out something about a nucleotide or amino acid sequence, employing in silico biology techniques. You may have sequenced a gene yourself, and wish to learn what the long string of letters representing bases, actually code for. You may want to confirm that you have indeed cloned a gene successfully, or you might want to learn about a sequence of DNA that you know absolutely nothing about. You may want to know if a worm has a similar protein to a human one. These, and many other situations, require that you employ sequence analysis.
http://www.sequenceanalysis.com/
Added: Fri Sep 27 2002, Hits: 3281, Reviews: 0 Write review Cached -
PolyPro - Polynucleotide probe design
In situ hybridization of genes and mRNA is most often based on polynucleotide probes. However, the specificity of polynucleotide probes has not been thoroughly investigated and a rational probe design concept was still missing, because the well established concept for oligonucleotide probe design cannot be transferred to polynucleotides. We recently developed a concept and software (PolyPro) for rational design of polynucleotide probe mixes to identify particular genes in defined taxa. PolyPro consists of three modules: a GenBank Taxonomy Extractor (GTE), a Polynucleotide Probe Designer (PPD) and a Hybridization Parameters Calculator (HPC).
http://www.dnabaser.com/PolyPro/index.html
Added: Mon Sep 10 2012, Hits: 53, Reviews: 0 Write review Cached -
Clone Library Dereplicator
When building clone libraries it is often the case that many of the sequenced clones are 100% identical. Therefore, before further DNA sequence analysis, it is necessary to find duplicate DNA sequences and remove them. Our DNA sequence dereplication tool sorts all unique DNA sequences (FASTA) belonging to your clone libraries, by moving/coping them into the specified folder. Clone Library Dereplicator simplifies the dereplication of all type sequence libraries (16S rRNA, 18S rRNA, 23S rRNA, 28S rRNA, functional and structural proteins) and prepares the raw sequences for subsequent analyses or contig assembly.
http://www.dnabaser.com/help/tools/tool-sequence-d...
Added: Mon Sep 10 2012, Hits: 46, Reviews: 0 Write review Cached -
Flexible Sequence Similarity Searching with the FASTA3 Program Package
(Humana Press )
provides a “hands on” overview of the programs in the FASTA package. Rather than discuss in depth the theory and practice of protein and DNA sequence comparison, this protocol focus on more practical questions, such as: “Which FASTA program should I use?”, “What threshold should I use for statistical significance?”, “Which databases should I search?”, “When should I use FASTA and when should I use BLAST?”, and “When should I change the scoring matrix and gap penalties?”
http://www.humanapress.com/pdfs/ch10185-.pdf
Added: Sun Jul 21 2002, Hits: 1350, Reviews: 0 Write review -
GenBank to Fasta Converter
GenBank to Fasta Converter is a a freeware molecular biology tool that can convert GenBank (gb/gbk) file format to FASTA format.
http://www.dnabaser.com/download/GBK-converter/ind...
Added: Mon Sep 10 2012, Hits: 56, Reviews: 0 Write review Cached -
Protein sequence analysis - A practical guide
(Terri Attwood and Alex Michie )
This is an interactive exercise that aims to provide a taste of bioinformatics resources around the world by introducing a range of widely-used analysis tools and databases.
http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/pref...
Added: Sat Sep 28 2002, Hits: 2213, Reviews: 0 Write review