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.
To extract all of the CDS, mRNA and the protein translations:
% coderet Extract CDS, mRNA and translations from feature tables Input sequence(s): tembl:X03487 Output sequence [hsferg1.fasta]: Output file [hsferg1.coderet]: |
Go to the input files for this example
Go to the output files for this example
Example 2
To only extract the mRNA sequence:
% coderet -nocds -notranslation Extract CDS, mRNA and translations from feature tables Input sequence(s): tembl:X03487 Output sequence [hsferg1.fasta]: Output file [hsferg1.coderet]: |
Go to the output files for this example
Standard (Mandatory) qualifiers: [-seqall] seqall Sequence database USA [-outseq] seqout Output sequence USA [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -[no]cds boolean Extract CDS sequences -[no]mrna boolean Extract mrna sequences -[no]translation boolean Extract translated sequences Associated qualifiers: "-seqall" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outseq" associated qualifiers -osformat2 string Output seq format -osextension2 string File name extension -osname2 string Base file name -osdirectory2 string Output directory -osdbname2 string Database name to add -ossingle2 boolean Separate file for each entry -oufo2 string UFO features -offormat2 string Features format -ofname2 string Features file name -ofdirectory2 string Output directory "-outfile" associated qualifiers -odirectory3 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-seqall] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
[-outfile] (Parameter 3) |
Output file name | Output file | <sequence>.coderet |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-[no]cds | Extract CDS sequences | Boolean value Yes/No | Yes |
-[no]mrna | Extract mrna sequences | Boolean value Yes/No | Yes |
-[no]translation | Extract translated sequences | Boolean value Yes/No | Yes |
ID HSFERG1 standard; DNA; HUM; 512 BP. XX AC X03487; XX SV X03487.1 XX DT 02-JUL-1986 (Rel. 09, Created) DT 04-APR-1995 (Rel. 43, Last updated, Version 2) XX DE Human apoferritin H gene exon 1 XX KW ferritin. XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Primates; Catarrhini; Hominidae; Homo. XX RN [1] RP 1-512 RX MEDLINE; 86120367. RA Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R., RA Delius H., Cortese R.; RT "Structure of gene and pseudogenes of human apoferritin H"; RL Nucleic Acids Res. 14:721-736(1986). XX DR EPD; EP11112; HS_FRIH. DR SWISS-PROT; P02794; FRIH_HUMAN. XX 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" XX SQ Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other; agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca 60 gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt 120 ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca 180 gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg 240 gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg 300 caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc 360 gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga 420 actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct 480 cctacgttta cctgtccatg gtgagcgcgg gc 512 // |
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.
>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 |
CDS mRNA Trans Total Sequence ===== ===== ===== ===== ======== 1 1 1 3 HSFERG1 |
>x03487_mrna_1 cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc ctcctacgtttacctgtccatg |
mRNA Total Sequence ===== ===== ======== 1 1 HSFERG1 |
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 sequence with restriction sites, translation etc |
showfeat | Show features of a sequence |
showorf | Pretty output of DNA translations |
showseq | Display a sequence with features, translation etc |
sixpack | Display a DNA sequence with 6-frame translation and ORFs |
transeq | Translate nucleic acid sequences |
twofeat | Finds neighbouring pairs of features in sequences |