Brief Guideline on

DNAMAN for Windows (Version 4, Lynnon BioSoft)

 based on Guideline Book and experience

Loading file:

Sequence/load sequence/from sequence (or other e.g. from Genbank file)/click your file and open/   

                     Sequence/display /DNA sequence and composition (Forward primer) or Rev. Compl. Sequence (Reverse primer)/ Save (.seq).

*Copy sequence from other source original: Edit/enter sequence/paste(Ctrl V)/Ok/Save(this time is tif file, you must rename file, then input “.seq” behind file name)

Sequence alignment:

Sequenc/ alignment/multiple sequence alignment/Add from file(selecting file name aligned, then selecting method:aligned; DNA; fast alignment)/OK/output/ Tree/homology Tree or phylogenetic tree/To bootstrap the tree, enter trial number(1-60000): 1000 usully/OK(waiting for 2 second for processing/ phylogenetic tree(Rooted tree;bootstrapping)

For detail, eg for some parameters selection, see Guideline book.

(To find primer sequence from output or the other windows: edit/find/input primer sequence or primer Rev.Compl.sequence because that Rev.Compl.chain was sometime sequenced)

Synthesize a sequence from two sequences of forward and reverse primer

 Sequenc/ alignment/multiple sequence alignment/Add from file(selecting file name of two sequences of forward and reverse primer, then selecting method:aligned; DNA; fast alignment)/OK/Output/sequence file/two sequence alignment/OK (show identity with ….) selecting sequence expected (the complete sequence between two sequences of forward and reverse primers: Find position of forward and reverse primers in sequence by search primer sequence or its Rev.Compl. Sequence. Note: 1. must search from begin of sequence; 2. sometime can find whole primer sequence, can search in part sequence of primer) /copy(Ctrl C)/text/

 Edit/enter sequence/past (Ctrl V)/OK/save/give a new file name.

Aligning and search sequence or related homology sequence from database through BLAST

Open website: http://www.ncbi.nlm.nih.gov/BLAST/

Search for short nearly exact matches

Past (Ctrl V) your sequence or corresponding embank entry into search box

BLAST

Format (waiting some time for auto-searching in database)

Results of Blast

Selecting results or related sequence

Save as /giving a file name (usually database number) (this time,file is .txt file)

Chang “.txt” into”.seq” file by rename