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coderet |
This specifies that the coding sequence for the gene is constructed by joining several sections of code, many of which are in other entries in this database.
FT CDS join(U21925.1:818..987,U21926.1:258..420, FT U21927.1:428..520,U21928.1:196..336,U21929.1:279..415, FT U21930.1:895..1014,516..708)
or:
This specifies that the messenger RNA sequence for the gene is constructed by joining several sections of code, many of which are in other entries in this database.
FT mRNA join(M88628.1:1006..1318,M88629.1:221..342, FT M88630.1:101..223,M88631.1:46..258,M88632.1:104..172, FT M88633.1:387..503,M88634.1:51..272,M88635.1:303..564, FT M88635.1:849..1020,M88636.1:282..375,M88637.1:39..253, FT M88638.1:91..241,M88639.1:168..377,M88640.1:627..3732, FT M88641.1:158..311,M88642.1:1051..1263,M88642.1:1550..1778, FT M88642.1:1986..2168,M88642.1:3904..4020, FT M88642.1:4627..4698,M88643.1:39..124,M88644.1:42..197, FT M88645.1:542..686,M88646.1:75..223,M88647.1:109..285, FT 253..2211)
or:
This specifies that the translation of the coding region is as follows.
FT /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEFL FT RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQN FT SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELRE FT NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFEA FT VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSSL FT PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTYF FT PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIHF FT GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSRS FT SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAEI FT THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"
It is often a tedious and error-prone job to extract the several sections of these sequences from the database entries and to join them together to construct the indicated finished sequence.
coderet does this job for you.
You specify the sequence containing the feature table and it extracts the required CDS, mRNA and/or protein sequences specified by this feature table. If any sequences are in other entries of that database, they are automatically fetched and incorporated correctly into the final sequence.
The translations are not made from the coding sequence, they are extracted directly from the translation sequence held in the feature table.
The EMBL sequence X03487's feature table is as follows:
FH Key Location/Qualifiers FH FT source 1..512 FT /db_xref="taxon:9606" FT /organism="Homo sapiens" FT misc_feature 65..70 FT /note="GGGCGG box" FT misc_feature 103..108 FT /note="GGGCGG box" FT misc_feature 126..131 FT /note="GGGCGG box" FT promoter 150..154 FT /note="put. TATA box" FT mRNA 179..500 FT /note="exon 1" FT CDS join(387..500,X03488.1:50..196,X03488.1:453..578, FT X03488.1:674..838) FT /db_xref="SWISS-PROT:P02794" FT /label=apoh_cds FT /product="apoferritin H subunit" FT /protein_id="CAA27205.1" FT /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD FT DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA FT LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE FT SGLAEYLFDKHTLGDSDNES" FT intron 501..>512 FT /note="intron I"
This means that the mRNA sequence is from position 179 to 500 in this sequence.
The coding sequence is formed by joining the region from 387 to 500 in this sequence together with regions from two other entries in this database: X03488 and X03488.
The translation of the coding sequence is also given.
To extract all of the CDS, mRNA and the protein translations, type:
% coderet Extract CDS, mRNA and translations from feature tables Input sequence(s): embl:X03487 Output sequence [hsferg1.fasta]:
The result is as follows:
>x03487_cds_1 atgacgaccgcgtccacctcgcaggtgcgccagaactaccaccaggactcagaggccgcc atcaaccgccagatcaacctggagctctacgcctcctacgtttacctgtccatgtcttac tactttgaccgcgatgatgtggctttgaagaactttgccaaatactttcttcaccaatct catgaggagagggaacatgctgagaaactgatgaagctgcagaaccaacgaggtggccga atcttccttcaggatatcaagaaaccagactgtgatgactgggagagcgggctgaatgca atggagtgtgcattacatttggaaaaaaatgtgaatcagtcactactggaactgcacaaa ctggccactgacaaaaatgacccccatttgtgtgacttcattgagacacattacctgaat gagcaggtgaaagccatcaaagaattgggtgaccacgtgaccaacttgcgcaagatggga gcgcccgaatctggcttggcggaatatctctttgacaagcacaccctgggagacagtgat aatgaaagctaa >x03487_mrna_1 cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc ctcctacgtttacctgtccatg >x03487_pro_1 MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHK LATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSD NES
Note that there is a mixture of nucleic and protein sequences in this file
To only extract the mRNA sequence, type:
% coderet -nocds -notranslation Extract CDS, mRNA and translations from feature tables Input sequence(s): embl:X03487 Output sequence [hsferg1.fasta]:
Mandatory qualifiers: [-seqall] seqall Sequence database USA [-seqout] seqout Output sequence USA Optional qualifiers: (none) Advanced qualifiers: -[no]cds boolean Extract CDS sequences -[no]mrna boolean Extract mrna sequences -[no]translation boolean Extract translated sequences General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-seqall] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-seqout] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-[no]cds | Extract CDS sequences | Yes/No | Yes |
-[no]mrna | Extract mrna sequences | Yes/No | Yes |
-[no]translation | Extract translated sequences | Yes/No | Yes |
One or more of CDS, mRNA, translation can be excluded from the output by using the appropriate qualifiers to the program (i.e. -nocds, etc.)
The ID names of the output sequences are constructed from the name of the input sequence, the type of feature being output (i.e. cds, mrna, pro) and a unique ordinal number for this type to distinguish it from others in this sequence. The name, type and number of separated by underscore characters. Thus the second CDS feature in the sequence 'HSXYZ' would be named 'HSXYZ_cds_2'.
The translations are not made from the coding sequence, they are extracted directly from the translation sequence held in the feature table.
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
extractfeat | Extract features from a sequence |
maskfeat | Mask off features of a sequence |
plotorf | Plot potential open reading frames |
prettyseq | Output sequence with translated ranges |
remap | Display a sequence with restriction cut sites, translation etc |
showfeat | Show features of a sequence |
showorf | Pretty output of DNA translations |
showseq | Display a sequence with features, translation etc |
swissparse | Retrieves sequences from swissprot using keyword search |
transeq | Translate nucleic acid sequences |