EMBL coding sequences (CDS) to Mauve XMFA alignment converter

Convert a EMBL coding sequences (CDS) sequence file to Mauve XMFA alignment.

Convert from Convert to Choose your sequence file

Maximum file size: 50 MB. The file is checked before conversion.

EMBL coding sequences (CDS) → Mauve XMFA alignment

Each CDS feature becomes one protein record built from its stated translation; the rest of the source record is not converted.
The selected output is an alignment format. Every sequence must be the same length and already aligned. This does not create an alignment.
The output keeps only each record's ID, so description text (such as the words after the ID on a FASTA header line) is not kept.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The notes under the Convert file button list the important limits for this pair.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.

from Bio import SeqIO

count = SeqIO.convert("input.embl-cds", "embl-cds",
                      "output.mauve", "mauve")
print("Converted %i records" % count)

Sample input file: EMBL coding sequences (CDS)

Copy this example into a file, or download it, to try a EMBL coding sequences (CDS) conversion.

ID   AAA03323; SV 1; linear; unassigned DNA; STD; INV; 1545 BP.
XX
PA   U01210.1
XX
DE   Anopheles merus alpha-amylase
XX
OS   Anopheles merus
OC   Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera;
OC   Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae;
OC   Anopheles.
OX   NCBI_TaxID=30066;
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1545
FT                   /organism="Anopheles merus"
FT                   /mol_type="unassigned DNA"
FT                   /clone_lib="V-12"
FT                   /clone="s1/pg155/Hd4"
FT   CDS             U01210.1:1212..2756
FT                   /codon_start=1
FT                   /gene="amy"
FT                   /standard_name="amylase"
FT                   /product="alpha-amylase"
FT                   /function="digestive enzyme"
FT                   /db_xref="GOA:Q17059"
FT                   /db_xref="HSSP:P56634"
FT                   /db_xref="InterPro:IPR006046"
FT                   /db_xref="InterPro:IPR006047"
FT                   /db_xref="InterPro:IPR006048"
FT                   /db_xref="InterPro:IPR006589"
FT                   /db_xref="InterPro:IPR013780"
FT                   /db_xref="InterPro:IPR013781"
FT                   /db_xref="UniProtKB/TrEMBL:Q17059"
FT                   /protein_id="AAA03323.1"
FT                   /translation="MKLLVRLAPILLLALTGRPVAAQHDPHFVRGHSTIVHLFEWKWSD
FT                   IADECERFLGPKGYGGVQLSPVNENIVIRLADGSRPWWERYQPISFKLDTRSGSEAEFA
FT                   DMSRRCNAAGVRLYVDIIINHMGATQPVEPAIGTGSSTAIPSDRQFPAVPFGWPDFNPP
FT                   CAINDWGNAEQIRNCELVGLHDLNQAVPWVRDRVVDFLNHLIELGVAGFRVDAAKHMWP
FT                   ADLAVIFGRLNNLNTAYGFAPGSRAFLAQEVIDMGAHEVVRKFEYTFLGTVTEFMFSHY
FT                   LGRAFGGNDALRWLSNFGEAWGLLASRDAFVFVDNHDNQRGNYGILTYKQPKPYKMATA
FT                   FAAAYPYGQLRIMSSFAFTDFDQGPPSDAQGNLLSPIINPDKTCGGGWVCEHRWRQMYS
FT                   MIHFRNLAWGTPLQHWWDNGNNQIAFARGNVGFVAFNNEPFDMNVILQTGLPAGIYCDV
FT                   ISGAREGETCTGLQVIVEPNGFASISIRANAEDGVIAIHSEVSVCVCCRMRSDGRV"
XX
SQ   Sequence 1545 BP; 287 A; 437 C; 498 G; 323 T; 0 other; 2371371509 CRC32;
     atgaagcttt tagtgcgcct agcaccgatc ctgctgctag ccctaaccgg tcgcccggta        60
     gccgctcagc acgatcccca ctttgtccgc ggccacagca cgatcgtgca tctgttcgag       120
     tggaaatgga gcgacattgc ggacgagtgt gagcgcttcc tggggcccaa agggtacggc       180
     ggtgtgcagc tgtctccagt gaacgagaac atcgtcattc gactggccga tggatctcgg       240
     ccgtggtggg aacggtatca gccaatttcc ttcaagctgg acacgcgatc gggctcggag       300
     gctgagtttg cggacatgtc gcggcgctgc aatgcggccg gcgtgcgtct gtacgtggac       360
     atcatcatca accacatggg agcgacgcaa cccgtcgagc cagcgatcgg tacgggaagt       420
     tccacggcca ttccctcgga ccgtcagttc ccggcggtac cgttcggatg gcccgacttt       480
     aacccaccgt gtgccatcaa cgattggggc aatgcggagc agatccggaa ctgtgagctg       540
     gtggggctgc acgatctgaa ccaggcggtg ccgtgggtgc gtgaccgtgt cgttgacttc       600
     ctgaaccatc tgatcgagct cggagtggcc ggattccgcg tggatgcggc caaacacatg       660
     tggcccgccg atctggcggt gatcttcgga cggctcaaca acctcaacac tgcgtacggg       720
     tttgcgccgg gatcgcgcgc attcctcgcg caggaagtca tcgatatggg ggcgcacgaa       780
     gtggttcgca agtttgagta cacgttcctc ggcacagtga cggagtttat gttctcgcac       840
     tatcttggtc gtgccttcgg tggaaatgac gcgctccgct ggctgtcgaa ctttggcgaa       900
     gcgtggggcc tgctggcgtc ccgcgatgcg ttcgtgttcg tggacaatca cgacaatcag       960
     cgcggtaact atggtattct cacgtacaaa cagcccaaac cgtacaagat ggccaccgcg      1020
     tttgcggccg cgtatccgta cggccagctg cgcatcatga gctcgttcgc gttcaccgac      1080
     tttgaccagg gcccgccgtc cgatgcgcag ggcaacctgc tgtcgcccat catcaatccg      1140
     gacaagacgt gcggcggcgg ctgggtgtgc gagcaccggt ggcgccagat gtacagcatg      1200
     atccacttcc gcaaccttgc ctggggtacg ccgctgcagc actggtggga caatggcaac      1260
     aaccagatcg cgtttgcccg cgggaacgtc ggctttgtgg cgttcaacaa cgaaccgttc      1320
     gacatgaacg tgatcttgca gacggggctg ccggccggta tctactgtga tgtgatttcg      1380
     ggtgctcgcg agggcgaaac gtgcaccggg ctgcaggtga ttgtagagcc gaacgggttc      1440
     gcttcgattt ctatccgagc caacgcggag gacggtgtga ttgcgatcca cagtgaggta      1500
     agtgtgtgtg tgtgttgccg aatgaggtct gatggccggg tgtga                      1545
//

Download sample (sample.embl, 4.2 KB)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

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