Gblock multiple alignment

Question

[baurumon]

HI,

I am using multiple alignment of non coding sequence to select conserved block. All the sequence has different length and when i run command : Gblocks result.pir -t=d -e=-gb1 -b4=5 -d=y, it is not accepting my data and showing---

Sequences with different number of positions. Execution terminated.

Is there any way to process data in Gblock?

Thanks in advance.

[GenoMax]

Have you tried to use the web interface to make sure your data is in correct format?

[baurumon]

i tried it but did not work.

I converted my .fasta file to .pir with EMBL sequence conversion tool. https://www.ebi.ac.uk/Tools/sfc/ . Sequences look like as below-

>D1;3amexicanus
, 119 bases
 AGAAGCCAGC TCTGAAGAAA GTGCGCATGT CTGCTGACGC TATGCTGCAA
 GCTCTGCTCG GCTCCAAACA CAAGGTGTCA ATGGACCTGA GGGCCAACCT
 CAAACAAGTC AAGAAGGAG*

>D1;4amexicanus
, 127 bases
 AGAGGCATGA AGGTCATTGA GAACAGGGCA CTGAAGGATG AGGAGAAGAT
 GGAGCTGCAA GAGATCCAGC TCAAAGAGGC CAAACACATT GCTGAGGAAG
 CTGATCGCAA ATATGAGGAA GTGAGTT*

>D1;5amexicanus
, 519 bases
 GGTCTAATGT TCATTCCTTG TGTTTCTTGG CCCAAACAAA TCTCTTCTGC
 TTGTTGCCTT TCCTAAGCAG TGGATTCCTA GCAGCTATTT GATCATGAAG
 GCCTGATTTG CGCCTTAGTC TCCTCTTAAC AGTTGTTCTA GAGATGTGTC
 TGCTGCTAGA ACTCTGTGTG GCATTCAACT GCTCTCTGAT CTgagctgct
 gttaacttgc ggtttctgag gctggtgact CGGATGTACT TATCCTGAGA
 AGCAGCAGAG gtgactcttg gtcttccttt cctgggttgG TCTTCATGTG
 TGCCAGTTTC GCTGTAGCGC TTGATGGTTT TTGTGACTCC ACTTGGGgac
 acatttaaag tttttgcaat tttctggact gactgacctt catttcttaa
 agtaatggTG GCCACTCATT TTTCTTTAGT TAGCTGAttg gttcttgcca
 taatatgaat tttaacagtt gtCCAATAAG GCTGTCGGGT GTGTAATAAC
 CAGACTTCTG CGCAACACA*

[baurumon]

Thank you @genomax

Answer 1

[GenoMax]

You need to input an alignment in .pir format not plain fasta sequences converted to .pir format for this tool.