Table 1

Summary of XplorSeq functionality

Function

Description1


Import

Chromatogram...

Import DNA chromatograms (.esd, .scf, .abi etc.): phred

PHD...

Import DNA sequences in Phd format

Contig...

Import DNA sequences and quality scores in FastA format

Blast...

Parse Blast records

FastA...

Import DNA sequences in FastA format

XplorSeq Library...

Import XplorSeq document

Phylogenetic Lineage...

Import phylogenetic lineage information from entrez

Metadata...

Import metadata in key-value format


Export

Sequences...

Export DNA sequences in variety of formats

FastA + Qual...

Export DNA sequences and quality scores

Blast Info...

Export summary of Blast records

Cluster Table...

Enumerate OTUs belonging to groups of sequences

OTU Diversity...

Calculate OTU richness for set of sequences

Quality Scores...

Export summary of quality scores

Blast Accession #'s...

Export accession numbers of top Blast hits

Sequin Script...

Export data in format for Genbank submission (sequin)

Blast Database...

Create a Blast database (formatdb)

XML File...

Export data in XML format

Metadata...

Summarize and export metadata

Placeholder Tree...

List selected sequences in Newick format


Analyze

Basecall->Blast...

Pipe data from chromatogram through Blast analysis

Contig->Blast...

Pipe data from contig assembly to Blast analysis

Basecall...

Perform base calling (phred or ttuner)

Contig...

Perform contig assembly (phrap or TIGR_Assembler)

Blast NCBI...

Blast query of Genbank

Blast Local...

Blast query of local blast database

Get Entrez Lineage Info.

Download entrez phylogenetic lineage information (idfetch)

Align...

Perform multiple sequence alignment (clustal)

Biodiversity (biodiv)...

Calculates biodiversity indices with random resampling (biodiv)

XplorSeq Doc Difference...

Generate differences between two XplorSeq documents


Transform

Edit Sequence Names...

Alter names of sequences

Edit Lineage Names...

Edit phylogenetic lineage information

Edit Metadata...

Edit metadata associated with sequence

Edit Metadata Keys...

Edit all metadata keys in document

Group...

Group sequences and contigs

UnGroup...

Ungroup sequences and contigs

Clean...

Delete blast information, contigs

Sort...

Sort records in document

Set Oligos...

Associate primer sequences with sequence objects

Trim...

Trim sequences based on quality score and primer

UnTrim.

Remove trimming information

Rev.-Complement

Reverse complement sequence

DNA -> RNA

Convert DNA sequence to RNA sequence

RNA -> DNA

Convert RNA sequence to DNA sequence

UPPER CASE

Convert sequence to upper case

lower case

Convert sequence to lower case


Alignment Analysis

OTU clustering

Cluster Operational Taxonomic Units (sortx)

Clearcut NJ Tree...

Fast neighbor joining trees (clearcut)

Phylip distance matrix...

Calculate distance matrix (dnadist)

Phylip NJ Tree...

Calculate Neighbor joining or UPGMA trees (neighbor)

Phylip seqboot...

Generate bootstrap replicates of alignment (seqboot)

Phylip consense...

Generate consensus of multiple trees (consense)

RAxML...

Generate Maximum Likelihood tree (raxmlHPC)


1Command line executables are listed in parentheses.

Frank BMC Bioinformatics 2008 9:420   doi:10.1186/1471-2105-9-420

Open Data