Converting CLUSTAL Format

Converting CLUSTAL Format

The sequence alignment outputs from CLUSTAL software often are given the default extension .aln. CLUSTAL is an interleaved format. In a page-wide arrangement the sequence name is in the first column and a part of the sequence’s data is right justified. An example of the CLUSTAL format follows:

CLUSTAL X (1.8) multiple sequence alignment

Q9Y2J0_Has   ------------MTDTVFSNSSNRWMYPSDRPLQSNDKEQLQAGWSVHPG

Q06846_RP3A_BOVIN  ------------MTDTVFSSSSSRWMCPSDRPLQSNDKEQLQTGWSVHPS

JX0338_rabphilin-3A-mouse  ------------MTDTVVN----RWMYPGDGPLQSNDKEQLQAGWSVHPG

Q9Y2J0_Has   GQPDRQRKQEELTDEEKEIINRVIARAEKMEEMEQER--IGRLVDRLENM

Q06846_RP3A_BOVIN  GQPDRQRKQEELTDEEKEIINRVIARAEKMEEMEQER--IGRLVDRLENM

JX0338_rabphilin-3A-mouse AQTDRQRKQEELTDEEKEIINRVIARAEKMEAMEQER--IGRLVDRLETM

The CLUSTAL file above would be converted by MEGA into the following format:

#mega

Title: Bigrab2.aln

#Q9Y2J0_Hsa

------------MTDTVFSNSSNRWMYPSDRPLQSNDKEQLQAGWSVHPG

GQPDRQRKQEELTDEEKEIINRVIARAEKMEEMEQER--IGRLVDRLENM

RKNVAGDGVNRCILCGEQLGMLGSACVVCEDCKKNVCTKCGVET-NNRLH

#Q06846_RP3A_BOVIN

------------MTDTVFSSSSSRWMCPSDRPLQSNDKEQLQTGWSVHPS

GQPDRQRKQEELTDEEKEIINRVIARAEKMEEMEQER--IGRLVDRLENM

RKNVAGDGVNRCILCGEQLGMLGSACVVCEDCKKNVCTKCGVETSNNRPH

#JX0338_rabphilin-3A-mouse

------------MTDTVVN----RWMYPGDGPLQSNDKEQLQAGWSVHPG

AQTDRQRKQEELTDEEKEIINRVIARAEKMEAMEQER--IGRLVDRLETM

RKNVAGDGVNRCILCGEQLGMLGSACVVCEDCKKNVCTKCGVETSNNRPH