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Genome Evolution Analysis
Welcome to CoGe -- a new system for a new kind of comparative genomics. CoGe is designed for easily visualizing, comparing, and understanding the evolution, struture and dynamics of genomes. Unfortunately, we have detected that your browser currently has JavaScript disabled. In order for CoGe to function properly, JavaScript must be enabled in your browser. For instruction on how to do so in Mozilla Firefox, please click
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Work Name:
Description:
Notes:
GEvo Configuration:
Run GEvo Analysis!
Sequence Submission
Algorithm
Results Visualization Options
Add Sequence
Merge Previous GEvo Analysis (paste in URL):
Merge
Change order by dragging boxes
Sequence 1:
CoGe Database Name
NCBI GenBank
Direct Submission
Display Order
Name:
Organism:
Position:
Chr:
Left sequence:
Right sequence:
Get Sequence
Genome View
Accession:
Start Position:
Sequence Length:
Paste fasta or genbank format sequence below:
Start:
Length:
Sequence Skipped
Sequence 1 Options
Skip Sequence:
Yes
No
Reference Sequence:
Yes
No
Reverse complement:
Yes
No
Mask Sequence:
--None--
CDS
All RNA
Non-CDS
Non-genic
Sequence 2:
CoGe Database Name
NCBI GenBank
Direct Submission
Display Order
Name:
Organism:
Position:
Chr:
Left sequence:
Right sequence:
Get Sequence
Genome View
Accession:
Start Position:
Sequence Length:
Paste fasta or genbank format sequence below:
Start:
Length:
Sequence Skipped
Sequence 2 Options
Skip Sequence:
Yes
No
Reference Sequence:
Yes
No
Reverse complement:
Yes
No
Mask Sequence:
--None--
CDS
All RNA
Non-CDS
Non-genic
Open all sequence option menus
Close all sequence option menus
Walk all sequences left
Walk all sequences right
Apply distance to all CoGe submissions?
Pad CoGe Sequences with additional sequence:
E-mail GEvo results?
Your E-mail Address:
You have supplied an invalid e-mail address.
Alignment Algorithm:
-=None=-
BlastN: Small Regions
(B)LastZ: Large Regions
Chaos: Fuzzy Matches
GenomeThreader - Spliced Gene Alignments
Lagan: Global Alignment
TBlastX: Protein Translation
Match Score (-r):
Mismatch Penalty (-q):
Gap Open Penalty (-G):
Gap Extension Penalty (-E):
Word Size (-W):
Filter query sequence (DUST/SEG) (-F):
Yes
No
Expectation value (-e):
Other Blast Parameters:
Hide HSPs with stop codons in a coding sequence?
Yes
No
Note: Word size limited to 3 for tblastx
Word size:
Score cutoff:
Rescore cutoff:
Lookback distance:
(length between seed alignments for chaining)
Maximum gap length between seeds for chaining:
Gap start penality:
Gap extend penality:
Other CHAOS parameters:
HSP filter by spike sequence
(set to 0 to turn off):
Spike sequence length:
nucleotides
Word size:
Gap start penality:
Gap extend penality:
Chaining:
no chaining
just output chain
chain and extend
just output HSPs
Score threshold:
Mask threshold:
Other Blastz parameters:
Min HSP Length:
Max Contiguous Gaps in HSPs:
Min Percent Identity:
Other LAGAN Parameters:
Use Anchored Alignment:
Use Anchored Search
Do NOT use Anchored Search
Min Alignment Score:
Max Contiguous Low Score Alignments in HSPs:
Split HSPs on Different Alignment Scores:
Yes
No
Aligment Method:
Short Sequence Alignment, No Translation
Short Sequence Alignment with Translation
Long Sequence Alignment
Use Motif in Alignment:
Yes
No
Motif:
Weighting Factor:
Distance Penalty:
Other DiAlign Parameters:
Note
: Using Translation Increases CDS Alignment Accuracy at Cost of Speed - Not Recommended for Sequences > 10 kb
Genome Threader
will find splice alignments of protein sequences to a genomic sequence.
Select Anchor Program:
blastz
bl2seq
CHAOS
Other options:
Minimum HSP length for finding overlapped features:
Image Width (Pixels):
Feature Height (Pixels):
Padding between tracks (Pixels):
Color
GC
content green? (SLOW)
Yes
No
Color
masked
and
unsequenced
NTs?
Yes
No
Color wobble codon GC content:
Yes
No
Color contigs
red
:
Yes
No
Auto adjust overlapping features?
Yes
No
Auto adjust overlapping HSPs (SLOW)?
Yes
No
Draw high-quality images? (SLOW)
Yes
No
Draw all HSPs on top?
Yes
No
Color features overlapped by HSPs?
Yes
No
Color matches in HSPs?
Yes
No
Label HSPs?
No
Draw Staggered
Draw Linear
Label Genomic Features?
No
Draw Staggered
Draw Linear
Labels font size:
Don't show HSPs with
overlaps
Don't show HSPs that are shorter than
nt.
(0 means no limit)
Draw:
Complete
Gene
mRNA
CDS
RNA
No
Models
Show pre-annotated CNSs?
Yes
No
Show pre-annotated Gene spaces?
Yes
No
Change HSP colors
(Click Color to Adjust)
HSP 1 color:
Run GEvo Analysis!
Date: 2012-02-12 18:49:22
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Genome Evolution Analysis
Genome Evolution Analysis