Sequencher

2015-01-13

azim58 - Sequencher

Sequencher Program
used for sequence (like DNA sequence analysis)

computers with sequencher in cim
bio4048456 (the computer next to Felicia)
bio6158009
This computer is physically loaded in Preston's old cubicle (B230AA). It
is a huge "workstation" computer located underneath the desk.

Example Sequencher Session

Note about sequencher orientation
Once sequencher includes sequences into a contig it sets the sequences in
a certain orientation. When that contig is dissolved, the sequences will
still be in the orientation that was set when they were a part of a
contig, which is not something I originally expected.
Also, Andrey mentioned that when several sequences are joined into a
contig the majority orientation will become the forward orientation. If
the orientation set is not what the user intended, the user can change it
by going to something like View->Reverse and Complement which will change
everything. Another way of dealing with this situation is to combine just
a few sequences into a contig to set the proper orientation, and then add
more sequences later after the orientation has been set.

Note about manually adding a sequence to a contig for manual alignment
Contig->Assemble Contig->Mindlessly join
Then the contig can be aligned using delete insert and shift features
(tab or shift+tab)

Note about finding a sequence in sequencher regardless of whether or not
the sequence is separated by gaps from the alignment
find a sequence that may be gapped with other characters

Comparison of Sequencher and Clustal Omega

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