XplorSeq protocols

View XplorSeq computational protocol

XplorSeq statistics

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XplorSeq specifications

Information


Unique identifier OMICS_15082
Name XplorSeq
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data DNA sequences
Input format FASTA
Output data Identity and phylogenetic lineage of the sequence's closest BLAST hit, BLAST statistics
Operating system Unix/Linux, Mac OS
Programming languages C, C++
Computer skills Medium
Stability No
Maintained No

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Publication for XplorSeq

XplorSeq in pipelines

 (3)
2015
PMCID: 4513208
PMID: 26092755
DOI: 10.1007/s00253-015-6729-4

[…] and sequencing were performed as described by sahl and colleagues (). sanger reads were called with phred (ewing et al. ; ewing and green ) and assembled with phrap (www.phrap.org) via xplorseq (frank ). identification of cultivar sequences was accomplished by parsimony addition into the silva ssuref108_nr database (pruesse et al. ) via arb (ludwig et al. ) and blast (altschul et […]

2012
PMCID: 3526174
PMID: 22832344
DOI: 10.1038/ismej.2012.79

[…] at the joint genome institute (under the community sequencing program) using standard protocols for the megabace4000 capillary electrophoresis platform. sequences were assembled by phrap using xplorseq (). 454 amplicon production was performed as previously described using barcoded 27f/338r primers targeting the v1/2 region of the bacterial 16s rrna gene (). sequencing was performed per […]

2009
PMCID: 2771765
PMID: 19907661
DOI: 10.1371/journal.pone.0007811

[…] megabace 1000 (amersham biosciences, piscataway, nj) automated dna sequencers., sequence base calling and contig assembly were performed with the applications phred and phrap , , as implemented by xplorseq . vector and primer sequences were removed along with flanking nucleotides of poor quality (q<20). initial microbial species identifications were made by a batch blast search […]


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XplorSeq in publications

 (8)
PMCID: 4513208
PMID: 26092755
DOI: 10.1007/s00253-015-6729-4

[…] and sequencing were performed as described by sahl and colleagues (). sanger reads were called with phred (ewing et al. ; ewing and green ) and assembled with phrap (www.phrap.org) via xplorseq (frank ). identification of cultivar sequences was accomplished by parsimony addition into the silva ssuref108_nr database (pruesse et al. ) via arb (ludwig et al. ) and blast (altschul et […]

PMCID: 3526174
PMID: 22832344
DOI: 10.1038/ismej.2012.79

[…] at the joint genome institute (under the community sequencing program) using standard protocols for the megabace4000 capillary electrophoresis platform. sequences were assembled by phrap using xplorseq (). 454 amplicon production was performed as previously described using barcoded 27f/338r primers targeting the v1/2 region of the bacterial 16s rrna gene (). sequencing was performed per […]

PMCID: 3189942
PMID: 22016793
DOI: 10.1371/journal.pone.0025959

[…] shannon diversity and chao1 were computed, using rarefaction (100 replicates) to compensate for differences in number of sequences per sample, using the biodiv functionality contained within the xplorseq toolkit , ., data were presented graphically, and descriptive statistics were calculated using sas v 9.2 (cary, nc). the percent of total sequence count was calculated for each individual […]

PMCID: 3100341
PMID: 21629788
DOI: 10.1371/journal.pone.0020296

[…] younger than 18 years. assent was obtained from all participants under 18 years., contiguous small subunit ribosomal rna sequences from multiple sequencing reactions were assembled using the program xplorseq 2.0 and compared to a database of well-curated sequences of isolates derived from silva 93 using blast to determine their approximate phylogenetic relationships. sequences were aligned […]

PMCID: 2871794
PMID: 20498722
DOI: 10.1371/journal.pone.0010598

[…] a megabace 1000 (amersham biosciences, piscataway, nj) automated dna sequencer. sequence base calling and contig assembly were performed with the applications phred and phrap , , as implemented by xplorseq . vector and primer sequences were removed along with poor quality flanking nucleotides (q<20)., all sequences were aligned to the silva ssuref version 98 database using the sina […]


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XplorSeq institution(s)
Department of Molecular, Cellular, and Developmental Biology, Mucosal and Vaccine Research Program Colorado, University of Colorado, Boulder, CO, USA

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