PubMed

A software pipeline for processing and identification of fungal ITS sequences.

Nilsson RH, Bok G, Ryberg M, Kristiansson E, Hallenberg N.

Source Code Biol Med. 2009 Jan 15;4:1.PMID: 19146660 [PubMed - in process]Related articlesFree article

Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi.

Nilsson RH, Kristiansson E, Ryberg M, Larsson KH.

BMC Bioinformatics. 2005 Jul 18;6:178.PMID: 16022740 [PubMed - indexed for MEDLINE]Related articlesFree article

galaxieEST: addressing EST identity through automated phylogenetic analysis.

Nilsson RH, Rajashekar B, Larsson KH, Ursing BM.

BMC Bioinformatics. 2004 Jul 5;5:87.PMID: 15236648 [PubMed - indexed for MEDLINE]Related articlesFree article

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219.PMID: 19607672 [PubMed - indexed for MEDLINE]Related articlesFree article

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.

Kõljalg U, Larsson KH, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AF, Tedersoo L, Vrålstad T, Ursing BM.

New Phytol. 2005 Jun;166(3):1063-8.PMID: 15869663 [PubMed - indexed for MEDLINE]Related articles

Assessment of ribosomal large-subunit D1-D2, internal transcribed spacer 1, and internal transcribed spacer 2 regions as targets for molecular identification of medically important Aspergillus species.

Hinrikson HP, Hurst SF, Lott TJ, Warnock DW, Morrison CJ.

J Clin Microbiol. 2005 May;43(5):2092-103.PMID: 15872227 [PubMed - indexed for MEDLINE]Related articlesFree article

TaxMan: a taxonomic database manager.

Jones M, Blaxter M.

BMC Bioinformatics. 2006 Dec 18;7:536.PMID: 17176465 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of dermatophytes by sequence analysis of the rRNA gene internal transcribed spacer regions.

Li HC, Bouchara JP, Hsu MM, Barton R, Su S, Chang TC.

J Med Microbiol. 2008 May;57(Pt 5):592-600.PMID: 18436592 [PubMed - indexed for MEDLINE]Related articlesFree article

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

Kohany O, Gentles AJ, Hankus L, Jurka J.

BMC Bioinformatics. 2006 Oct 25;7:474.PMID: 17064419 [PubMed - indexed for MEDLINE]Related articlesFree article

PDA: a pipeline to explore and estimate polymorphism in large DNA databases.

Casillas S, Barbadilla A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W166-9.PMID: 15215372 [PubMed - indexed for MEDLINE]Related articlesFree article

Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.

Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson KH, Kõljalg U.

PLoS One. 2006 Dec 20;1:e59.PMID: 17183689 [PubMed - in process]Related articlesFree article

Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota).

Ryberg M, Nilsson RH, Kristiansson E, Töpel M, Jacobsson S, Larsson E.

BMC Evol Biol. 2008 Feb 18;8:50.PMID: 18282272 [PubMed - indexed for MEDLINE]Related articlesFree article

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.

Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E.

FEMS Microbiol Lett. 2009 Jul;296(1):97-101. Epub 2009 May 1.PMID: 19459974 [PubMed - indexed for MEDLINE]Related articles

Computational identification of strain-, species- and genus-specific proteins.

Mazumder R, Natale DA, Murthy S, Thiagarajan R, Wu CH.

BMC Bioinformatics. 2005 Nov 23;6:279.PMID: 16305751 [PubMed - indexed for MEDLINE]Related articlesFree article

XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.

Frank DN.

BMC Bioinformatics. 2008 Oct 7;9:420.PMID: 18840282 [PubMed - indexed for MEDLINE]Related articlesFree article

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST.

Kim YJ, Boyd A, Athey BD, Patel JM.

Nucleic Acids Res. 2005 Aug 1;33(13):4335-44. Print 2005.PMID: 16061938 [PubMed - indexed for MEDLINE]Related articlesFree article

Database indexing for production MegaBLAST searches.

Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA.

Bioinformatics. 2008 Aug 15;24(16):1757-64. Epub 2008 Jun 21. Erratum in: Bioinformatics. 2008 Dec 15;24(24):2942. PMID: 18567917 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogeny.fr: robust phylogenetic analysis for the non-specialist.

Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19.PMID: 18424797 [PubMed - indexed for MEDLINE]Related articlesFree article

An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity.

Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH.

New Phytol. 2009 Jan;181(2):471-7.PMID: 19121041 [PubMed - indexed for MEDLINE]Related articles

FastBLAST: homology relationships for millions of proteins.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2008;3(10):e3589. Epub 2008 Oct 31.PMID: 18974889 [PubMed - indexed for MEDLINE]Related articlesFree article