Difference between revisions of "References"

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== Tools Used in CoGe ==
 
== Tools Used in CoGe ==
  
* BLAST
+
{| border="1" cellspacing="0"
** Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ  (1990)  Basic local alignment search tool. Journal of Molecular Biology 215:403-410
+
! Tool
* BlastZ
+
! Reference
** Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W  (2003)  Human-mouse alignments with BLASTZ. Genome Research 13:103-7
+
|-
* DAGChainer
+
| BLAST
** Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20: 3643–3646
+
| Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ  (1990)  Basic local alignment search tool. Journal of Molecular Biology 215:403-410
* ClustalW
+
|-
** Thompson JD, Higgins DG, Gibson TJ  (1994)  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680
+
| BlastZ
* CHAOS
+
| Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W  (2003)  Human-mouse alignments with BLASTZ. Genome Research 13:103-7
** Brudno M., Chapman M., Göttgens B., Batzoglou S., Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003;4:66
+
|-
* DIALIGN 2
+
| DAGChainer
** Morgenstern, B. (1999). DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211–218
+
| Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20: 3643–3646
* JalView
+
|-
* NJPlot
+
| ClustalW
 +
| Thompson JD, Higgins DG, Gibson TJ  (1994)  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680
 +
|-
 +
| CHAOS
 +
| Brudno M., Chapman M., Göttgens B., Batzoglou S., Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003;4:66
 +
|-
 +
| DIALIGN 2
 +
| Morgenstern, B. (1999). DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211–218
 +
|-
 +
| JalView
 +
|-
 +
| NJPlot
 +
|}
  
 
== Genomes Used in CoGe ==
 
== Genomes Used in CoGe ==
  
 
Unfortunately, due to the large number of genomes currently stored in CoGe (currently over 6,600), we cannot list all the references here. However, we are currently working on a system to automate the production of citations for searches. In the meantime, we urge you to find these citations on your own if you are to publish work based on data obtained from these genomes in addition to citing CoGe.
 
Unfortunately, due to the large number of genomes currently stored in CoGe (currently over 6,600), we cannot list all the references here. However, we are currently working on a system to automate the production of citations for searches. In the meantime, we urge you to find these citations on your own if you are to publish work based on data obtained from these genomes in addition to citing CoGe.

Revision as of 20:07, 12 August 2009

Here you can find a list of references to be cited whenever using a CoGe tool.

CoGe References

  • Lyons E, Freeling M (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal 53:661-673
  • Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D. (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids, Plant Phys 148, pp. 1772–1781.

Tools Used in CoGe

Tool Reference
BLAST Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215:403-410
BlastZ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W (2003) Human-mouse alignments with BLASTZ. Genome Research 13:103-7
DAGChainer Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20: 3643–3646
ClustalW Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680
CHAOS Brudno M., Chapman M., Göttgens B., Batzoglou S., Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003;4:66
DIALIGN 2 Morgenstern, B. (1999). DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211–218
JalView
NJPlot

Genomes Used in CoGe

Unfortunately, due to the large number of genomes currently stored in CoGe (currently over 6,600), we cannot list all the references here. However, we are currently working on a system to automate the production of citations for searches. In the meantime, we urge you to find these citations on your own if you are to publish work based on data obtained from these genomes in addition to citing CoGe.