Seqret

BioCodeKb - Bioinformatics Knowledgebase

EMBOSS Seqret reads and writes (returns) sequences. It is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.


seqret reads in one or more sequences and writes them out again. The sequence input may be a literal sequence or read from a database, file, file of sequence names, or even the command-line or the output of another programs. The sequence output can be written to screen, to file, or passed to another program. A wide range of standard sequence formats may be specified for input and output. If you we don’t  specify the input format, seqret will try a set of possible formats until it reads it in successfully. The sequence input and output, as for all EMBOSS programs, is described by a Uniform Sequence Address. This is is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications.


The output is a standard EMBOSS sequence file.


The results can be output in one of many styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.


In some cases the output filename will be the same as the input filename, but as seqret reads only the first sequence before opening the output file it may try to overwrite the input.


Step 1: Input Sequences

Input Sequence

One or more sequences to be translated can be entered directly into this form. Sequences can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input.


Sequence File Upload

A file containing one or more valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be uploaded and used as input for the translation. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.


Sequence Type

Shows if the query sequence is protein, DNA or RNA. Used to force FASTA to interpret the input sequence as specified type of sequence (via. the '-p', '-n' or '-U' options), this prevents issues when using nucleotide sequences that contain many ambiguous residues.


Step 2: Select parameters

Input Format

Input format name

List Input Formats

Default value is: Unknown format


Output Format

Output format name.

List Output Formats

Default value is: EMBL entry format [embl]


Feature Selection

Use feature information. Values yes / no

Default value is: yes [true]


First Sequence Only

Read one sequence and stop. Values yes / no

Default value is: no [false]


Reverse-Complement of Input Sequencess

Reverse-complement of input DNA sequences. Values yes / no

Default value is: no [false]


Output Case

Change alphabet case for output sequences. Values No change, lower case, UPPER CASE

Default value is: No change [none]


Sequence Range

Specify a range or section of the input sequence to use in the search. sequence of total length 100, will tell EMBOSS seqret to only use residues 34 to 89, inclusive.

Default value is: START-END


Step 3: Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.


Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

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