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the separation sign or string in MAF(mult.align)

Dear biostar community,

I've read the answers to this Question:

Perl How To Isolate Fasta Sequences With A Specific Keyword

Fortunately, we have a separation block sign '>' in fasta.

I have a huge maf (multiple alignments) from UCSC-database, and I need to do about the same - to find the multiple alignments with some particular key-words.

Is there the separation sign between different multiple alignments in maf?

Knowing the starting symbol or starting string, I would try something like that:

# reading from input-file
while($line=<IN>) {
        next if $line =~ /^\s$/;
# skip empty line
        next if ($line =~ /No hits/);
        if($line =~ /^>/) {
#start a new block

But what should I do for maf?

Please, help me!

Thank you very much,

Natasha

alignment
• 301 views • link
updated by Ram Ram • written by natasha.sernova natasha.sernova

Please flag your previous question as answered.

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

what would be a 'keyword' in tha following maf ?

##maf version=1 scoring=autoMZ.v1
a score=-6945.000000
s dm3.chr2R                       0 36 +  21146708 GACCCGCTAGGAGATGTTGAGATTGTGAGTA------CTTCT
s droMoj3.scaffold_6482     2566883 36 -   2735782 gatccaatgggtgaagtagaaatagtaacct------catca
i droMoj3.scaffold_6482   N 0 C 0
s droWil1.scaffold_180786      3982 36 -     25716 gatccaatgggtgaagtggaagtagtagcct------cctca
i droWil1.scaffold_180786 N 0 C 0
s droPer1.super_54            63154 36 +    518223 gacccgatgggggatgttgaaatagtcgcct------catcc
i droPer1.super_54        N 0 C 0
s dp4.Unknown_group_55         1887 36 +     31046 GAACCGATGGGGGAGGTTGAAATATTCACCT------CATCC
i dp4.Unknown_group_55    N 0 C 0
s droAna3.scaffold_13077     423351 36 -    610351 gatccgatgggagacatagaattgg------tttcatcctca
i droAna3.scaffold_13077  N 0 C 0
s apiMel3.GroupUn         345083485 23 - 399230636 ------------GATGCTGAAACTCAAATTT------TTCT-
i apiMel3.GroupUn         N 0 I 2
s droYak2.chrU             25873964 12 -  28119190 -------------------------tgggttt-----gtctt
i droYak2.chrU            N 0 C 0
s droSim1.chrU              5338042  5 +  15797150 -------------------------------------cccct
i droSim1.chrU            N 0 C 0

a score=16867.000000
s dm3.chr2R                      36 39 +  21146708 TGGAATTTGGTTATCT------ATTATAAAATGG----ATCCATATTTT-------
s droAna3.scaffold_13077     423387 39 -    610351 tggaatttagtgatat------tgtacgatatgg----aagcatatttc-------
i droAna3.scaffold_13077  C 0 C 0
s droSim1.chrU              5338047 39 +  15797150 tggaacttagtagctt------actaaaatctga----acgtctatttt-------
i droSim1.chrU            C 0 C 0
s droYak2.chrU             25873976 37 -  28119190 agcaatgcagttattt------ata------ttgtgttgtgaattttct-------
i droYak2.chrU            C 0 C 0
s dp4.Unknown_group_55         1923 39 +     31046 TGGGATTTAATTGTTT------ATTATAACATGG----ACCCGTATTTC-------
i dp4.Unknown_group_55    C 0 C 0
s droPer1.super_54            63190 39 +    518223 tgggatttaattgttt------attataaaatgg----acccgtatttc-------
i droPer1.super_54        C 0 C 0
s droWil1.scaffold_180786      4018 39 -     25716 tgggatctggtaatat------actatgacatgt----cggcatatttt-------
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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