GCG 程式: SeqEd

簡介

產生 GCG 序列檔案格式的一種方法是利用 GCG 套組中的 SeqEd 編輯器輸入序列，這樣在檔案產生時就會自動計算「checksum」。 SeqEd 編輯器有兩種使用模式，一是全螢幕編輯模式，另一是指令模式。前者讓使用者能自由在螢幕上游走編輯；後者則讓使用者做輸入、輸出、尋找線上輔助系統、或大範圍的刪除等工作。

啟動程式時會進入指令模式，只需將游標移入編輯區即進入全螢幕模式。若要回到指令模式，只需同時按下ctrl-D 兩鍵即可，此時游標會回到瑩幕左下角的冒號後等待你輸入指令。 在指令行鍵入 help，即可在使用程式時看到說明:

使用編輯器時通常是先在提示符號 (％) 後鍵入 SeqEd 及檔案名，程式找不到這個檔，就會問你是否要開新檔案。在回答「是」後即可輸入備註，輸入後或是不想輸入，可將游標移到序列區，直接鍵入序列。在序列輸入結束後，按「ctrl-D」即可跳入指令全螢幕模式。在此模式下可儲存檔案 (write)，退出系統 (quit)，或先存檔再退出 (Exit)。

練習1 請利用 SeqEd 程式輸入「CHFENCG」，並將檔案命名為「pep2.pro」

「Answers: 請依下列步驟建立新檔案
1. %seqed pep2.pro
2.是(建立新檔)
3.輸入備註 (comments)
4.輸入序列
5.ctrl-D 進入指令模式
6.Exit...............」

全螢幕模式(指令模式，回到檔頭)

Screen Mode

　 　 [n] is an optional numeric parameter.
　 　 　

G, A, T,... -

 　 insert a sequence character

<Delete> -

 　 delete a sequence character

<Ctrl>H -

 　 delete a sequence character

/TAACG<Return> -

 　 find the next occurrence of TAACG
　 　 (last pattern entered is the default)

1<Return> -

 　 move to start of the sequence

<Ctrl>E -

 　 move to end of the sequence

[n]<Right-arrow> -

 　 go ahead n characters

[n]<Left-arrow> -

 　 go back n characters

<Up-arrow> -

 　 go up to check sequence

<Down-arrow> -

 　 go down to original sequence

'markcharacter -

 　 go to marked position

37<Return> -

 　 go to position 37 (any positive integer)

< -

 　 go back 50 characters

> -

 　 go ahead 50 characters

<Ctrl>R -

 　 redraw the screen

<Ctrl>D -

 　 enter command mode

指令模式 (全螢幕模式，回到檔頭)

Command Mode
Commands end with . [n] indicates an optional parameter.
s and f are numbers for start and finish of a range of interest
Only the capitalized part of the command is necessary.
EDit seqname - get a new sequence file to edit
[n] Include [seqname] - insert another sequence [at position n]
(SeqEd prompts for range and strand)
s,f Delete - delete a range of bases
[s] Check [/Blind] - check a range of bases [beginning at s]
37 - go to base 37
REDraw - redraw the screen
[n] COmment comment - insert a comment [at position n]
[n] COmment - enter comment editing mode [at position n]
[n] HEAding - edit documentary heading [at line n]
change - enter screen mode ( is sufficient)
screen - enter screen mode ( is sufficient)
OVERstrike - enter overstrike mode
INSert - enter insert mode
[n] Mark markcharacter - mark the sequence [at position n]
PERFect - require finds to be perfect matches
PROtein - set sequence type to PROTEIN
NUCleotide - set sequence type to NUCLEOTIDE
[s,f] Write [seqname] - write [a part of] the sequence to a file
DIGitizer - enter digitizer mode
RELoad - enter reload mode
ACCept - terminate reload mode
Help - show commands in screen and command modes
[s,f] EXit [seqname] - write [a part of] the sequence and quit
Quit - quit the editor without writing the sequence
Press to return to SEQED:

　

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Last updated on 11/23/01