• AlignExIn
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Usage

You can start the application either directly by clicking on "Start Application" or download the program archive by clicking on "Download Application" and start it manually on your computer by entering

java -jar alignexin.jar

in a terminal. If it does not work, maybe you should add the folder where the file has been downloaded before alignexin.jar.

In the menu option "Edit" you can

• Change Colors: Specify which amount of red, green or blue should be taken for either exon or alignment. Note: the values MUST be in the range 0 to 255!
• Set Parameters: specify height of exon or alignemnt (in pixels).

Input

The are two different input files: the alignments file in fasta format the and exon positions.

Alignment File

The alignments file must have the folowing structure

>Triboliumcastaneum
M--------------------------V------------------------------VL
LFC-TG-IPHLARPFPRLFEEHAELLTLFEKF---KELKTKEDQANSLELAEHASTVMNT
LDEGIKE-LDNLDTFFEYLHQVGASHRRIPGFKVEYFWKIEKPFLTAVETTLGDRYTENV
ENIYKITIKFIIETLVKGYDNA-N-A----------------------------P-T-
>Aedesaegypti
M-----------------------------------------------------------
-FCRTV-NIHVQTVTEELFEEHAELLEMFANF---KELKTKEEQATSEELQEHANKVMNT
LDEGIRG-LDDLDTFFEFIHQVGASHRRLPGFKQEYFWRIEEPFLSAVSNTLGDRYTQNV
EGIYKLTIKFIIETLVAGYESS-A-NNNEDVNNANLSTTGSAAGPTTSGD--KKT-S-
>AnophelesgambiaestrPEST
------------------------------------------------------------
---------------MTLFEEHADLLNMFAKF---KELKTKEEQATSEELQEHANKVMNT
LDEGIRG-LDDLDTFFEFIHQVGASHRRIPGFKQEYFWRIEEPFLSAVSTTLGDRYTQNV
EGIYKLTIKFIIETLVAGYEAS-A-NNNVDNT------TSSSTPATKLSDEPNRA-S-

Especially the header should only contain the ">" and the name.

Exon File

The exon file contains the exon parts (start and end positions separated by commas) like

Triboliumcastaneum=1:19,20:97,98:144
Aedesaegypti=1:6,7:16,17:94,95:167
AnophelesgambiaestrPEST=3:80,81:149

Blanks are not considered and the names in the fasta file headers must correspondend to the names in the exon file.

Gaps in the alignment file have to be considered here! That means a range is calculated on every letter in the alignment and gaps like "-" are just "ignored". That means for the first line of the exons file (and I take only the first area!)

Triboliumcastaneum=1:19

The considered alignments are (written in lower letters)

>Triboliumcastaneum
m--------------------------v------------------------------vl
lfc-tg-iphlarpfprLFEEHAELLTLFEKF---KELKTKEDQANSLELAEHASTVMNT
LDEGIKE-LDNLDTFFEYLHQVGASHRRIPGFKVEYFWKIEKPFLTAVETTLGDRYTENV

Errors

In case of problems or failure this application produces a log file called alexin.log, which is stored in $HOME/.bioinf on Unix systems and the appropriate "Documents and Settings/user/.bioinf" folder on Windows computers. Attach this file reporting an error is useful for error debugging.