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Items: 1 to 20 of 122

1.

Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels.

Faircloth BC, Glenn TC.

PLoS One. 2012;7(8):e42543. doi: 10.1371/journal.pone.0042543. Epub 2012 Aug 10.

2.

Improved lower bounds of DNA tags based on a modified genetic algorithm.

Wang B, Wei X, Dong J, Zhang Q.

PLoS One. 2015 Feb 18;10(2):e0110640. doi: 10.1371/journal.pone.0110640. eCollection 2015. Erratum in: PLoS One. 2015;10(6):e0130784.

3.

OligoTag: a program for designing sets of tags for next-generation sequencing of multiplexed samples.

Coissac E.

Methods Mol Biol. 2012;888:13-31. doi: 10.1007/978-1-61779-870-2_2.

PMID:
22665273
4.

Novel software package for cross-platform transcriptome analysis (CPTRA).

Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. doi: 10.1186/1471-2105-10-S11-S16.

5.

Insertion and deletion correcting DNA barcodes based on watermarks.

Kracht D, Schober S.

BMC Bioinformatics. 2015 Feb 18;16:50. doi: 10.1186/s12859-015-0482-7.

6.

Computational identification and analysis of single-nucleotide polymorphisms and insertions/deletions in expressed sequence tag data of Eucalyptus.

Singh TR, Gupta A, Riju A, Mahalaxmi M, Seal A, Arunachalam V.

J Genet. 2011 Aug 18;90(2):e34-8. No abstract available.

7.
8.

Statistical modeling of sequencing errors in SAGE libraries.

Beissbarth T, Hyde L, Smyth GK, Job C, Boon WM, Tan SS, Scott HS, Speed TP.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i31-9.

PMID:
15262778
9.

Pooled library tissue tags for EST-based gene discovery.

Gavin AJ, Scheetz TE, Roberts CA, O'Leary B, Braun TA, Sheffield VC, Soares MB, Robinson JP, Casavant TL.

Bioinformatics. 2002 Sep;18(9):1162-6.

PMID:
12217907
10.

SPIDER: software for protein identification from sequence tags with de novo sequencing error.

Han Y, Ma B, Zhang K.

J Bioinform Comput Biol. 2005 Jun;3(3):697-716.

PMID:
16108090
11.

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.

Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW.

PLoS One. 2011;6(7):e22953. doi: 10.1371/journal.pone.0022953. Epub 2011 Jul 29.

12.

Obtaining accurate translations from expressed sequence tags.

Wasmuth J, Blaxter M.

Methods Mol Biol. 2009;533:221-39. doi: 10.1007/978-1-60327-136-3_10.

PMID:
19277570
13.

DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid.

Deng J, Huang H, Yu X, Jin J, Lin W, Li F, Song Z, Li M, Gan S.

BMC Bioinformatics. 2015 Oct 24;16:343. doi: 10.1186/s12859-015-0790-y.

14.

Levenshtein error-correcting barcodes for multiplexed DNA sequencing.

Buschmann T, Bystrykh LV.

BMC Bioinformatics. 2013 Sep 11;14:272. doi: 10.1186/1471-2105-14-272.

15.

Identifying and removing artificial replicates from 454 pyrosequencing data.

Teal TK, Schmidt TM.

Cold Spring Harb Protoc. 2010 Apr;2010(4):pdb.prot5409. doi: 10.1101/pdb.prot5409.

PMID:
20360363
16.

Correction of sequence-based artifacts in serial analysis of gene expression.

Akmaev VR, Wang CJ.

Bioinformatics. 2004 May 22;20(8):1254-63. Epub 2004 Feb 10.

PMID:
14871862
17.

[Transcriptomes for serial analysis of gene expression].

Marti J, Piquemal D, Manchon L, Commes T.

J Soc Biol. 2002;196(4):303-7. Review. French.

PMID:
12645300
18.

High-throughput identification, database storage and analysis of SNPs in EST sequences.

Useche FJ, Gao G, Harafey M, Rafalski A.

Genome Inform. 2001;12:194-203.

PMID:
11791238
19.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E.

PLoS One. 2007 Feb 14;2(2):e197.

20.

SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing.

Alexander AM, Pecoraro C, Styche A, Rudert WA, Benos PV, Ringquist S, Trucco M.

Biotechniques. 2005 Jan;38(1):87-94.

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