BioJava (Spanish Wikipedia)

Analysis of information sources in references of the Wikipedia article "BioJava" in Spanish language version.

refsWebsite

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16oxfordjournals.org

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1biomedcentral.com

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apache.org

maven.apache.org

Maven, Apache. «Maven». Apache.

biojava.org

«History». Consultado el 30 Jan 2015.
CookBook3, BioJava. «ModFinder».
CookBook3, BioJava. «Protein Disorder CLI».

biomedcentral.com

Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE (2005). «The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications». BMC Bioinformatics 6: 21. PMC 548701. PMID 15694009. doi:10.1186/1471-2105-6-21.

cshlp.org

genome.cshlp.org

Vernikos GS, Parkhill J (February 2008). «Resolving the structural features of genomic islands: a machine learning approach». Genome Res. 18 (2): 331-42. PMC 2203631. PMID 18071028. doi:10.1101/gr.7004508.
Stajich JE, Block D, Boulez K (October 2002). «The Bioperl toolkit: Perl modules for the life sciences». Genome Res. 12 (10): 1611-8. PMC 187536. PMID 12368254. doi:10.1101/gr.361602.
Stein LD, Mungall C, Shu S (October 2002). «The generic genome browser: a building block for a model organism system database». Genome Res. 12 (10): 1599-610. PMC 187535. PMID 12368253. doi:10.1101/gr.403602.

doi.org

dx.doi.org

Prlić A, Yates A, Bliven SE (October 2012). «BioJava: an open-source framework for bioinformatics in 2012». Bioinformatics 28 (20): 2693-5. PMC 3467744. PMID 22877863. doi:10.1093/bioinformatics/bts494.
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K (2008). «BioJava: an open-source framework for bioinformatics.». Bioinformatics 24 (18): 2096-7. PMC 2530884. PMID 18689808. doi:10.1093/bioinformatics/btn397.
Kim T, Tyndel MS, Huang H (March 2012). «MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets». Nucleic Acids Res. 40 (6): e47. PMC 3315295. PMID 22210894. doi:10.1093/nar/gkr1294.
Paterson T, Law A (November 2012). «JEnsembl: a version-aware Java API to Ensembl data systems». Bioinformatics 28 (21): 2724-31. PMC 3476335. PMID 22945789. doi:10.1093/bioinformatics/bts525.
Zajac P, Pettersson E, Gry M, Lundeberg J, Ahmadian A (February 2008). «Expression profiling of signature gene sets with trinucleotide threading». Genomics 91 (2): 209-17. PMID 18061398. doi:10.1016/j.ygeno.2007.10.012.
Vernikos GS, Parkhill J (February 2008). «Resolving the structural features of genomic islands: a machine learning approach». Genome Res. 18 (2): 331-42. PMC 2203631. PMID 18071028. doi:10.1101/gr.7004508.
Gront D, Kolinski A (February 2008). «Utility library for structural bioinformatics». Bioinformatics 24 (4): 584-5. PMID 18227118. doi:10.1093/bioinformatics/btm627.
Mangalam H (2002). «The Bio* toolkits--a brief overview.». BRIEFINGS IN BIOINFORMATICS 3 (3): 296-302. PMID 12230038. doi:10.1093/bib/3.3.296.
Cock PJ, Antao T, Chang JT (June 2009). «Biopython: freely available Python tools for computational molecular biology and bioinformatics». Bioinformatics 25 (11): 1422-3. PMC 2682512. PMID 19304878. doi:10.1093/bioinformatics/btp163.
Stajich JE, Block D, Boulez K (October 2002). «The Bioperl toolkit: Perl modules for the life sciences». Genome Res. 12 (10): 1611-8. PMC 187536. PMID 12368254. doi:10.1101/gr.361602.
Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T (October 2010). «BioRuby: bioinformatics software for the Ruby programming language». Bioinformatics 26 (20): 2617-9. PMC 2951089. PMID 20739307. doi:10.1093/bioinformatics/btq475.
Rice P, Longden I, Bleasby A (June 2000). «EMBOSS: the European Molecular Biology Open Software Suite». Trends Genet. 16 (6): 276-7. PMID 10827456. doi:10.1016/S0168-9525(00)02024-2.
Ye Y, Godzik A (October 2003). «Flexible structure alignment by chaining aligned fragment pairs allowing twists». Bioinformatics 19 (Suppl 2): ii246-55. PMID 14534198. doi:10.1093/bioinformatics/btg1086.
Shindyalov IN, Bourne PE (September 1998). «Protein structure alignment by incremental combinatorial extension (CE) of the optimal path». Protein Eng. 11 (9): 739-47. PMID 9796821. doi:10.1093/protein/11.9.739.
Bliven S, Prlić A (2012). «Circular permutation in proteins». PLoS Comput. Biol. 8 (3): e1002445. PMC 3320104. PMID 22496628. doi:10.1371/journal.pcbi.1002445.
Rose PW, Beran B, Bi C (January 2011). «The RCSB Protein Data Bank: redesigned web site and web services». Nucleic Acids Res. 39 (Database issue): D392-401. PMC 3013649. PMID 21036868. doi:10.1093/nar/gkq1021.
Prlic A, Bliven S, Rose PW (December 2010). «Pre-calculated protein structure alignments at the RCSB PDB website». Bioinformatics 26 (23): 2983-5. PMC 3003546. PMID 20937596. doi:10.1093/bioinformatics/btq572.
Bernstein FC, Koetzle TF, Williams GJ (May 1977). «The Protein Data Bank: a computer-based archival file for macromolecular structures». J. Mol. Biol. 112 (3): 535-42. PMID 875032. doi:10.1016/s0022-2836(77)80200-3.
Velankar S, McNeil P, Mittard-Runte V (January 2005). «E-MSD: an integrated data resource for bioinformatics». Nucleic Acids Res. 33 (Database issue): D262-5. PMC 540012. PMID 15608192. doi:10.1093/nar/gki058.
Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE (2005). «The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications». BMC Bioinformatics 6: 21. PMC 548701. PMID 15694009. doi:10.1186/1471-2105-6-21.
Besemer J, Borodovsky M (July 2005). «GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses». Nucleic Acids Res. 33 (Web Server issue): W451-4. PMC 1160247. PMID 15980510. doi:10.1093/nar/gki487.
Blanco E, Abril JF (2009). «Computational gene annotation in new genome assemblies using GeneID». Methods Mol. Biol. 537: 243-61. PMID 19378148. doi:10.1007/978-1-59745-251-9_12.
Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (January 2012). «Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering». Nucleic Acids Res. 40 (1): e9. PMC 3245904. PMID 22102569. doi:10.1093/nar/gkr1067.
Stein LD, Mungall C, Shu S (October 2002). «The generic genome browser: a building block for a model organism system database». Genome Res. 12 (10): 1599-610. PMC 187535. PMID 12368253. doi:10.1101/gr.403602.
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (April 2010). «The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants». Nucleic Acids Res. 38 (6): 1767-71. PMC 2847217. PMID 20015970. doi:10.1093/nar/gkp1137.
Needleman SB, Wunsch CD (March 1970). «A general method applicable to the search for similarities in the amino acid sequence of two proteins». J. Mol. Biol. 48 (3): 443-53. PMID 5420325. doi:10.1016/0022-2836(70)90057-4.
Smith TF, Waterman MS (March 1981). «Identification of common molecular subsequences». J. Mol. Biol. 147 (1): 195-7. PMID 7265238. doi:10.1016/0022-2836(81)90087-5.
Guan X, Uberbacher EC (February 1996). «Alignments of DNA and protein sequences containing frameshift errors». Comput. Appl. Biosci. 12 (1): 31-40. PMID 8670617. doi:10.1093/bioinformatics/12.1.31.
Chen K, Jung YS, Bonagura CA (February 2002). «Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential». J. Biol. Chem. 277 (7): 5603-10. PMID 11704670. doi:10.1074/jbc.M108916200.
Montecchi-Palazzi L, Beavis R, Binz PA (August 2008). «The PSI-MOD community standard for representation of protein modification data». Nat. Biotechnol. 26 (8): 864-6. PMID 18688235. doi:10.1038/nbt0808-864.
Garavelli JS (June 2004). «The RESID Database of Protein Modifications as a resource and annotation tool». Proteomics 4 (6): 1527-33. PMID 15174122. doi:10.1002/pmic.200300777.
Berman HM, Westbrook J, Feng Z (January 2000). «The Protein Data Bank». Nucleic Acids Res. 28 (1): 235-42. PMC 102472. PMID 10592235. doi:10.1093/nar/28.1.235.
Farriol-Mathis N, Garavelli JS, Boeckmann B (June 2004). «Annotation of post-translational modifications in the Swiss-Prot knowledge base». Proteomics 4 (6): 1537-50. PMID 15174124. doi:10.1002/pmic.200300764.
Yang ZR, Thomson R, McNeil P, Esnouf RM (August 2005). «RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins». Bioinformatics 21 (16): 3369-76. PMID 15947016. doi:10.1093/bioinformatics/bti534.
Finn RD, Clements J, Eddy SR (July 2011). «HMMER web server: interactive sequence similarity searching». Nucleic Acids Res. 39 (Web Server issue): W29-37. PMC 3125773. PMID 21593126. doi:10.1093/nar/gkr367.

elsevier.com

linkinghub.elsevier.com

Zajac P, Pettersson E, Gry M, Lundeberg J, Ahmadian A (February 2008). «Expression profiling of signature gene sets with trinucleotide threading». Genomics 91 (2): 209-17. PMID 18061398. doi:10.1016/j.ygeno.2007.10.012.
Rice P, Longden I, Bleasby A (June 2000). «EMBOSS: the European Molecular Biology Open Software Suite». Trends Genet. 16 (6): 276-7. PMID 10827456. doi:10.1016/S0168-9525(00)02024-2.
Needleman SB, Wunsch CD (March 1970). «A general method applicable to the search for similarities in the amino acid sequence of two proteins». J. Mol. Biol. 48 (3): 443-53. PMID 5420325. doi:10.1016/0022-2836(70)90057-4.
Smith TF, Waterman MS (March 1981). «Identification of common molecular subsequences». J. Mol. Biol. 147 (1): 195-7. PMID 7265238. doi:10.1016/0022-2836(81)90087-5.

jbc.org

Chen K, Jung YS, Bonagura CA (February 2002). «Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential». J. Biol. Chem. 277 (7): 5603-10. PMID 11704670. doi:10.1074/jbc.M108916200.

nih.gov

ncbi.nlm.nih.gov

Prlić A, Yates A, Bliven SE (October 2012). «BioJava: an open-source framework for bioinformatics in 2012». Bioinformatics 28 (20): 2693-5. PMC 3467744. PMID 22877863. doi:10.1093/bioinformatics/bts494.
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K (2008). «BioJava: an open-source framework for bioinformatics.». Bioinformatics 24 (18): 2096-7. PMC 2530884. PMID 18689808. doi:10.1093/bioinformatics/btn397.
Kim T, Tyndel MS, Huang H (March 2012). «MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets». Nucleic Acids Res. 40 (6): e47. PMC 3315295. PMID 22210894. doi:10.1093/nar/gkr1294.
Paterson T, Law A (November 2012). «JEnsembl: a version-aware Java API to Ensembl data systems». Bioinformatics 28 (21): 2724-31. PMC 3476335. PMID 22945789. doi:10.1093/bioinformatics/bts525.
Zajac P, Pettersson E, Gry M, Lundeberg J, Ahmadian A (February 2008). «Expression profiling of signature gene sets with trinucleotide threading». Genomics 91 (2): 209-17. PMID 18061398. doi:10.1016/j.ygeno.2007.10.012.
Vernikos GS, Parkhill J (February 2008). «Resolving the structural features of genomic islands: a machine learning approach». Genome Res. 18 (2): 331-42. PMC 2203631. PMID 18071028. doi:10.1101/gr.7004508.
Gront D, Kolinski A (February 2008). «Utility library for structural bioinformatics». Bioinformatics 24 (4): 584-5. PMID 18227118. doi:10.1093/bioinformatics/btm627.
Mangalam H (2002). «The Bio* toolkits--a brief overview.». BRIEFINGS IN BIOINFORMATICS 3 (3): 296-302. PMID 12230038. doi:10.1093/bib/3.3.296.
Cock PJ, Antao T, Chang JT (June 2009). «Biopython: freely available Python tools for computational molecular biology and bioinformatics». Bioinformatics 25 (11): 1422-3. PMC 2682512. PMID 19304878. doi:10.1093/bioinformatics/btp163.
Stajich JE, Block D, Boulez K (October 2002). «The Bioperl toolkit: Perl modules for the life sciences». Genome Res. 12 (10): 1611-8. PMC 187536. PMID 12368254. doi:10.1101/gr.361602.
Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T (October 2010). «BioRuby: bioinformatics software for the Ruby programming language». Bioinformatics 26 (20): 2617-9. PMC 2951089. PMID 20739307. doi:10.1093/bioinformatics/btq475.
Rice P, Longden I, Bleasby A (June 2000). «EMBOSS: the European Molecular Biology Open Software Suite». Trends Genet. 16 (6): 276-7. PMID 10827456. doi:10.1016/S0168-9525(00)02024-2.
Ye Y, Godzik A (October 2003). «Flexible structure alignment by chaining aligned fragment pairs allowing twists». Bioinformatics 19 (Suppl 2): ii246-55. PMID 14534198. doi:10.1093/bioinformatics/btg1086.
Shindyalov IN, Bourne PE (September 1998). «Protein structure alignment by incremental combinatorial extension (CE) of the optimal path». Protein Eng. 11 (9): 739-47. PMID 9796821. doi:10.1093/protein/11.9.739.
Bliven S, Prlić A (2012). «Circular permutation in proteins». PLoS Comput. Biol. 8 (3): e1002445. PMC 3320104. PMID 22496628. doi:10.1371/journal.pcbi.1002445.
Rose PW, Beran B, Bi C (January 2011). «The RCSB Protein Data Bank: redesigned web site and web services». Nucleic Acids Res. 39 (Database issue): D392-401. PMC 3013649. PMID 21036868. doi:10.1093/nar/gkq1021.
Prlic A, Bliven S, Rose PW (December 2010). «Pre-calculated protein structure alignments at the RCSB PDB website». Bioinformatics 26 (23): 2983-5. PMC 3003546. PMID 20937596. doi:10.1093/bioinformatics/btq572.
Bernstein FC, Koetzle TF, Williams GJ (May 1977). «The Protein Data Bank: a computer-based archival file for macromolecular structures». J. Mol. Biol. 112 (3): 535-42. PMID 875032. doi:10.1016/s0022-2836(77)80200-3.
Velankar S, McNeil P, Mittard-Runte V (January 2005). «E-MSD: an integrated data resource for bioinformatics». Nucleic Acids Res. 33 (Database issue): D262-5. PMC 540012. PMID 15608192. doi:10.1093/nar/gki058.
Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE (2005). «The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications». BMC Bioinformatics 6: 21. PMC 548701. PMID 15694009. doi:10.1186/1471-2105-6-21.
Besemer J, Borodovsky M (July 2005). «GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses». Nucleic Acids Res. 33 (Web Server issue): W451-4. PMC 1160247. PMID 15980510. doi:10.1093/nar/gki487.
Blanco E, Abril JF (2009). «Computational gene annotation in new genome assemblies using GeneID». Methods Mol. Biol. 537: 243-61. PMID 19378148. doi:10.1007/978-1-59745-251-9_12.
Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (January 2012). «Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering». Nucleic Acids Res. 40 (1): e9. PMC 3245904. PMID 22102569. doi:10.1093/nar/gkr1067.
Stein LD, Mungall C, Shu S (October 2002). «The generic genome browser: a building block for a model organism system database». Genome Res. 12 (10): 1599-610. PMC 187535. PMID 12368253. doi:10.1101/gr.403602.
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (April 2010). «The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants». Nucleic Acids Res. 38 (6): 1767-71. PMC 2847217. PMID 20015970. doi:10.1093/nar/gkp1137.
Needleman SB, Wunsch CD (March 1970). «A general method applicable to the search for similarities in the amino acid sequence of two proteins». J. Mol. Biol. 48 (3): 443-53. PMID 5420325. doi:10.1016/0022-2836(70)90057-4.
Smith TF, Waterman MS (March 1981). «Identification of common molecular subsequences». J. Mol. Biol. 147 (1): 195-7. PMID 7265238. doi:10.1016/0022-2836(81)90087-5.
Guan X, Uberbacher EC (February 1996). «Alignments of DNA and protein sequences containing frameshift errors». Comput. Appl. Biosci. 12 (1): 31-40. PMID 8670617. doi:10.1093/bioinformatics/12.1.31.
Chen K, Jung YS, Bonagura CA (February 2002). «Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential». J. Biol. Chem. 277 (7): 5603-10. PMID 11704670. doi:10.1074/jbc.M108916200.
Montecchi-Palazzi L, Beavis R, Binz PA (August 2008). «The PSI-MOD community standard for representation of protein modification data». Nat. Biotechnol. 26 (8): 864-6. PMID 18688235. doi:10.1038/nbt0808-864.
Garavelli JS (June 2004). «The RESID Database of Protein Modifications as a resource and annotation tool». Proteomics 4 (6): 1527-33. PMID 15174122. doi:10.1002/pmic.200300777.
Berman HM, Westbrook J, Feng Z (January 2000). «The Protein Data Bank». Nucleic Acids Res. 28 (1): 235-42. PMC 102472. PMID 10592235. doi:10.1093/nar/28.1.235.
Farriol-Mathis N, Garavelli JS, Boeckmann B (June 2004). «Annotation of post-translational modifications in the Swiss-Prot knowledge base». Proteomics 4 (6): 1537-50. PMID 15174124. doi:10.1002/pmic.200300764.
Yang ZR, Thomson R, McNeil P, Esnouf RM (August 2005). «RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins». Bioinformatics 21 (16): 3369-76. PMID 15947016. doi:10.1093/bioinformatics/bti534.
Finn RD, Clements J, Eddy SR (July 2011). «HMMER web server: interactive sequence similarity searching». Nucleic Acids Res. 39 (Web Server issue): W29-37. PMC 3125773. PMID 21593126. doi:10.1093/nar/gkr367.

oxfordjournals.org

bioinformatics.oxfordjournals.org

Prlić A, Yates A, Bliven SE (October 2012). «BioJava: an open-source framework for bioinformatics in 2012». Bioinformatics 28 (20): 2693-5. PMC 3467744. PMID 22877863. doi:10.1093/bioinformatics/bts494.
Paterson T, Law A (November 2012). «JEnsembl: a version-aware Java API to Ensembl data systems». Bioinformatics 28 (21): 2724-31. PMC 3476335. PMID 22945789. doi:10.1093/bioinformatics/bts525.
Gront D, Kolinski A (February 2008). «Utility library for structural bioinformatics». Bioinformatics 24 (4): 584-5. PMID 18227118. doi:10.1093/bioinformatics/btm627.
Cock PJ, Antao T, Chang JT (June 2009). «Biopython: freely available Python tools for computational molecular biology and bioinformatics». Bioinformatics 25 (11): 1422-3. PMC 2682512. PMID 19304878. doi:10.1093/bioinformatics/btp163.
Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T (October 2010). «BioRuby: bioinformatics software for the Ruby programming language». Bioinformatics 26 (20): 2617-9. PMC 2951089. PMID 20739307. doi:10.1093/bioinformatics/btq475.
Ye Y, Godzik A (October 2003). «Flexible structure alignment by chaining aligned fragment pairs allowing twists». Bioinformatics 19 (Suppl 2): ii246-55. PMID 14534198. doi:10.1093/bioinformatics/btg1086.
Prlic A, Bliven S, Rose PW (December 2010). «Pre-calculated protein structure alignments at the RCSB PDB website». Bioinformatics 26 (23): 2983-5. PMC 3003546. PMID 20937596. doi:10.1093/bioinformatics/btq572.
Yang ZR, Thomson R, McNeil P, Esnouf RM (August 2005). «RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins». Bioinformatics 21 (16): 3369-76. PMID 15947016. doi:10.1093/bioinformatics/bti534.

nar.oxfordjournals.org

Kim T, Tyndel MS, Huang H (March 2012). «MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets». Nucleic Acids Res. 40 (6): e47. PMC 3315295. PMID 22210894. doi:10.1093/nar/gkr1294.
Rose PW, Beran B, Bi C (January 2011). «The RCSB Protein Data Bank: redesigned web site and web services». Nucleic Acids Res. 39 (Database issue): D392-401. PMC 3013649. PMID 21036868. doi:10.1093/nar/gkq1021.
Velankar S, McNeil P, Mittard-Runte V (January 2005). «E-MSD: an integrated data resource for bioinformatics». Nucleic Acids Res. 33 (Database issue): D262-5. PMC 540012. PMID 15608192. doi:10.1093/nar/gki058.
Besemer J, Borodovsky M (July 2005). «GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses». Nucleic Acids Res. 33 (Web Server issue): W451-4. PMC 1160247. PMID 15980510. doi:10.1093/nar/gki487.
Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (January 2012). «Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering». Nucleic Acids Res. 40 (1): e9. PMC 3245904. PMID 22102569. doi:10.1093/nar/gkr1067.
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (April 2010). «The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants». Nucleic Acids Res. 38 (6): 1767-71. PMC 2847217. PMID 20015970. doi:10.1093/nar/gkp1137.
Finn RD, Clements J, Eddy SR (July 2011). «HMMER web server: interactive sequence similarity searching». Nucleic Acids Res. 39 (Web Server issue): W29-37. PMC 3125773. PMID 21593126. doi:10.1093/nar/gkr367.

peds.oxfordjournals.org

Shindyalov IN, Bourne PE (September 1998). «Protein structure alignment by incremental combinatorial extension (CE) of the optimal path». Protein Eng. 11 (9): 739-47. PMID 9796821. doi:10.1093/protein/11.9.739.

plos.org

dx.plos.org

Bliven S, Prlić A (2012). «Circular permutation in proteins». PLoS Comput. Biol. 8 (3): e1002445. PMC 3320104. PMID 22496628. doi:10.1371/journal.pcbi.1002445.