Difference between revisions of "FastaView"
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FastaView is CoGe's application for generating fasta formatted sequences from a list of genomic features. FastaView easily allows you to generate DNA sequence and protein sequence translations. If a sequence has only one reading frame (as determined by a starting methionine and no in-sequence stop codons), only that protein sequence will be shown. Otherwise FastaAlign will generate protein sequence (with stops) for all 6 reading frames. Sequences in FastaView can be easily copied from the text-box displaying the sequences by doubling clicking in the text-box. This will automatically select all the sequences in the text-box which can then be copied and pasted into another application. Alternatively, you can click on the "Plain Text" button and the sequences will be sent to a web-page only containing the sequences. This page can be saved for later used. | FastaView is CoGe's application for generating fasta formatted sequences from a list of genomic features. FastaView easily allows you to generate DNA sequence and protein sequence translations. If a sequence has only one reading frame (as determined by a starting methionine and no in-sequence stop codons), only that protein sequence will be shown. Otherwise FastaAlign will generate protein sequence (with stops) for all 6 reading frames. Sequences in FastaView can be easily copied from the text-box displaying the sequences by doubling clicking in the text-box. This will automatically select all the sequences in the text-box which can then be copied and pasted into another application. Alternatively, you can click on the "Plain Text" button and the sequences will be sent to a web-page only containing the sequences. This page can be saved for later used. | ||
| + | |||
| + | ==Links to external applications== | ||
| + | Since FastaView's main purpose is to retrieve sequence for use in other programs, we are happy to add links to other web-applications. Please contact [[Contact Page | Eric Lyons]] with your request. | ||
| + | |||
| + | Programs linked from FastaView: | ||
| + | *[http://target.iplantcollaborative.org/ TARGeT: Tree Analysis of Related Genes and Transposons] | ||
===Note:=== | ===Note:=== | ||
| − | FastaView is an intermediate application in CoGe that is usually accessed through another program, such as [FeatList]. | + | FastaView is an intermediate application in CoGe that is usually accessed through another program, such as [[FeatList]]. |
==Example Link== | ==Example Link== | ||
| − | You can view an example FastaView page | + | You can view an example FastaView page [http://synteny.cnr.berkeley.edu/CoGe/FastaView.pl?featid=4096250_1&featid=4084991_1&featid=4075625_1&featid=4091018_1&featid=4091015_1&featid=4075871_1&featid=4091276_1&featid=4078682_1&featid=4073195_1&featid=4073192_1&featid=4073198_1&featid=4073189_1&featid=4072826_1&featid=4086473_1&featid=4081526_1&featid=4081529_1&featid=4097339_1&featid=4097618_1&featid=4075373_1;gstid=1 here] |
Latest revision as of 12:59, 26 August 2009
FastaView is CoGe's application for generating fasta formatted sequences from a list of genomic features. FastaView easily allows you to generate DNA sequence and protein sequence translations. If a sequence has only one reading frame (as determined by a starting methionine and no in-sequence stop codons), only that protein sequence will be shown. Otherwise FastaAlign will generate protein sequence (with stops) for all 6 reading frames. Sequences in FastaView can be easily copied from the text-box displaying the sequences by doubling clicking in the text-box. This will automatically select all the sequences in the text-box which can then be copied and pasted into another application. Alternatively, you can click on the "Plain Text" button and the sequences will be sent to a web-page only containing the sequences. This page can be saved for later used.
Links to external applications
Since FastaView's main purpose is to retrieve sequence for use in other programs, we are happy to add links to other web-applications. Please contact Eric Lyons with your request.
Programs linked from FastaView:
Note:
FastaView is an intermediate application in CoGe that is usually accessed through another program, such as FeatList.
Example Link
You can view an example FastaView page here
