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Swaap 1.0.3

Swaap 1.0.3 was created to be an easy-to-use integrated package for the analysis of multiple alignments and bacterial genome sequences.  Its primary purpose is for sliding window analysis, to analyze trends in substitutions and similarity across multiple alignments, or trends in nucleotide usage patterns across bacterial genomes.  Most functions available in Swaap can be performed for entire genomes or multiple alignments, for portions of each, or with a sliding window approach.  Swaap has rudimentary plotting functions, however, it is designed to work with Microsoft Excel to analyze and plot resulting data.

    Multiple alignment functions available in Swaap:

• Nucleotide and amino acid identity
• Hydropathy index
• Evolutionary distances (4 methods available)
• Synonymous and nonsynonymous substitutions (3 methods available)
• Transitions and transversions (4 methods available)
• G + C content
• Codon usage and relative synonymous codon usage (RSCU)
• Pattern density (Markov chain and Zero-Order Markov available)
• Find sequences in alignments
• Translate nucleotide sequences
• Reverse, complement, and reverse-complement sequences
• Save sequences in different formats (3 formats available)
• Remove sequences from alignments
• Remove insertions and deletions from alignments
• Perform analysis by codon position 

    Bacterial genome functions available in Swaap:

• G + C content
• Pattern density (Markov chain and Zero-Order Markov available)
• GC and AT skew
• Oligonucleotide word frequencies (dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide) using 3 different methods (Markov Chain, Zero-Order Markov, and codon usage)
• Oligonucleotide difference index (oligonucleotides across sliding window)
• Removal of horizontal DNA (based on GC content, or tetranucleotide difference index) in genomes

Swaap was used in our recent publications:

    Pride, D.T., and M.J. Blaser (2002).  Concerted evolution between duplicated genetic elements in

                 Helicobacter pylori.  J Mol Biol. 316: 629-42.

    Pride, D.T., and M.J. Blaser (2002).  Identification of horizontally acquired genetic elements in 

                Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis.

                Genome Letters 1: 2-15.

    Ghose, C., G.I. Perez-Perez, M.G. Dominguez-Bella, D.T. Pride, C. Bravi, and M.J. Blaser (2002). 

                East Asian Genotypes of Helicobacter pylori strains in Amerindians provides evidence for its

                ancient human carriage.  PNAS 99: 15107-11

    Pride, D.T., R.J. Meinersmann, T.M. Wassenaar, and M.J. Blaser (2003).  Evolutionary implications 

                of microbial genome tetranucleotide frequency biases.  Genome Research 13: 145-58.

    Pride, D.T., T.M. Wassenaar, C. Ghose, and M. J. Blaser (2006).  Evidence of host-virus co-evolution

                in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses.  BMC Genomics 7: 8.

    Pride, D.T., and C. Ghose (2008).  Core genomic signature analysis in prokaryotes: what happens to

                phylogenetic signal when the horizontal DNA is gone?  In Progress.

Swaap is available for 32- bit Windows platforms only.

Download updated version Swaap version 1.0.3 (4.4mb zip file)

Tips for getting started:

•  If having problems with MSF file formats, convert multiple alignments to GDE format using ClustalX

• All bacterial genomes must begin with the word 'ORIGIN'

• Save genomes in Swaap Genome Format to avert converting the same genome multiple times

• Swaap does not interpret amino acid alignments, but does translate nucleotide alignments

• Swaap can only interpret multiple alignments with up to 300 different sequences

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Disclaimer

Swaap Phylogeny Helper (Swaap PH)

Swaap PH was created to analyze differences in patterns of nucleotide usage between coding and noncoding regions of microbial genomes, as well as to create distances between different microbes based on nucleotide usage differences.  The distances can be used as the basis for microbial phylogeny, using Phylip95 or Paup 4.0.  Swaap PH is designed to work in conjunction with Swaap for genome analysis.  Swaap PH also is capable of creating artificial bacterial genomes (pseudogenomes) based on several different criteria.  These pseudogenomes can be analyzed for patterns of nucleotide usage using Swaap, and compared with actual genome data.  The output of each analysis is designed to be used with Microsoft Excel.

    Bacterial genome functions available in Swaap PH for coding regions:

• G + C content analysis
• Analysis of G + C content deviation by codon position
• Analysis of G + C content deviation in reference to other genes
• Codon usage and RSCU analysis
• Codon usage and RSCU deviation analysis
• Oligonucleotide word deviation analysis (dinucleotide, trinucleotide, and tetranucleotide)
• Oligonucleotide word deviation analysis in reference to other genes
• Oligonucleotide word frequencies (dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide) using 2 different methods (Markov Chain, Zero-Order Markov)
• Tetranucleotide frequencies based on codon usage
• Sliding window analysis of transcription direction

    Bacterial genome functions available in Swaap PH for noncoding regions:

• Find noncoding regions (based on genbank annotation)
• G + C content
• Oligonucleotide word frequencies (dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide) using 3 different methods (Markov Chain, Zero-Order Markov)

    Bacterial genome functions available in Swaap PH for pseudogenome creation:

• Pseudogenome based on G + C content
• Pseudogenome based on codon usage
• Pseudogenome based on codon usage, retaining intergenic regions
• Pseudogenome based on dinucleotide usage
• Pseudogenome based on di-amino acid usage

    Bacterial genome functions available in Swaap PH for microbial phylogeny:

• Assemble files for distance matrix creation (dinucleotides, trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides)
• Distance matrix based on sum of differences in oligonucleotide frequencies (bootstrapping available)
• Distance matrix based on character states of oligonucleotide frequencies (2 character states - overrepresented and underrepresented)
• Extensive distance matrix based on character states of oligonucleotide frequencies (multiple character states based on the extent of over- and underpresentation of oligonucleotides)
• Distance matrix analysis after removal of aberrantly represented oligonucleotides

Swaap PH was used in our recent publications:

    Pride, D.T., and M.J. Blaser (2002).  Identification of horizontally acquired genetic elements in 

                Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis.

                Genome Letters 1: 2-15.

    Pride, D.T., R.J. Meinersmann, T.M. Wassenaar, and M.J. Blaser (2003).  Evolutionary implications 

                of microbial genome tetranucleotide frequency biases.  Genome Research 13: 145-58.

    Pride, D.T., T.M. Wassenaar, C. Ghose, and M. J. Blaser (2006).  Evidence of host-virus co-evolution

                in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses.  BMC Genomics 7: 8.

    Pride, D.T., and C. Ghose (2008).  Core genomic signature analysis in prokaryotes: what happens to

                phylogenetic signal when the horizontal DNA is gone?  In Progress.

Swaap PH is available for 32- bit Windows platforms only.

Download updated Swaap PH version 1.0.2 (4.5mb zip file)

Tips for getting started:

• All bacterial genome coding region files must begin with the word 'ORIGIN'

• Finding noncoding regions requires genomes in Swaap genome format (requires use of Swaap)

• Save data files, and open using Microsoft Excel

• Creation of di-amino acid genomes requires analysis of di-amino acids

• Distance files are created based on oligonucleotides requires use of the 'Input files' function under the 'Phylogeny' menu.  Files to be input are those saved files from analysis of oligonucleotides.  These files also can be created manually.  See help file for details.

• Swaap PH only interprets genomes with up to 8000 ORFs

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Swaap Genome Search 1.0.1

Swaap Genome Search was created to try to discern the host prokaryotes and the virus types of phage metagenome data, but can be used also for prokaryote metagenome data as well.  It is based on the concept of genome signature, where the program can read in metagenome contigs as FastA files, or in Swaap Genome Format, and compare the oligonucleotide signatures of those metagenome contigs with those of a prokaryote or virus database of signatures.  A phylogeny is then built based on these signatures, and the contigs are classified based on their phylogenetic position.

A tool for predicting prokaryote hosts of bacteriophages and discerning virus types from metagenome data

• Contains database of all sequenced prokaryotes

• Contains database of all sequenced virus genomes

• Applies phylogenetic reproduction techniques to predict ancestry of metagenome fragments

• Bootstrapping technique allows for statistical support for classifications

• Outputs phylogenies that can be viewed

Swaap Genome Search was used in our recent publications:

    Pride, D.T, and T. Schoenfeld (2008).  Genome signature analysis of thermal virus metagenomes reveals

            Archaea and thermophilic signatures.  BMC Genomics 9: 420.

Swaap Genome Search 1.01 is available for 32- bit Windows platforms only.

Download updated Swaap Genome Search 1.0.1 (242kb RAR  file)

Download contains help file and program file.

Download Swaap Genome databases last updated 5-5-08 (101mb RAR file)

Tips for getting started:

• Recognize that when looking at prokaryote database, analysis of single sequence will take at least 20-30 minutes

• Recognize that when looking at virus database, analysis of a single sequence will take at least 1.5 hours

• Recognize that when using bootstrapping technique, method takes at least the number of bootstraps as long

• Creating databases takes at least 24-28 hours

• Keep all database files in a single folder

• For longer sequences (>2.5kb, use tetranucleotide database).  Use trinucleotide database for shorter sequences

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Coming Soon!

Swaap Gene 1.0.0

One step phylogenetic reproduction using gene sequences

• Contains many of the same functions as Swaap, but reads up to 1000 sequences

• Phylogenies based on nucleotide alignments or pattern of nucleotide usage

• Available for 32-bit Windows platforms only

Disclaimer:

This software is supplied as-is, with no warranty of any kind expressed or implied.  I have made efforts to make it reliable, and to avoid errors, however but will not be liable for its use or misuse.  The user is solely responsible for the validity of any results generated.  Specifically, the author, Vanderbilt University, Stanford University, and The Bacteria Museum are not liable for any damage or loss of data resulting from use of this software, even if it is due to negligence on the part of the author of this software.

This software and this document are the responsibility of David T. Pride, MD PhD.  

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Page last modified: 19 September 2008