Readseq
Introduction
Readseq reads and converts biosequences between a selection of common biological sequence formats, including EMBL, GenBank and fasta sequence formats.
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How to use this tool
Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.
Each tool has at least 2 steps, but most of them have more:
- The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
- In the following steps, the user has the possibility to change the default tool parameters
- And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server
Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.
Step 1 - Input Sequences
Input Sequence
One or more sequences to be translated can be entered directly into this form. Sequences can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is a 2MB limit.
Sequence File Upload
A file containing one or more valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) 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. There is a 2MB limit.
Step 2 - Select parameters
Input Format
Input format name
| Format Name | Value |
|---|---|
| Auto-detected | 0 |
| EMBL | 4 |
| GenBank | 2 |
| Fasta(Pearson) | 8 |
| Clustal/ALN | 22 |
| ACEDB | 25 |
| BLAST | 20 |
| DNAStrider | 6 |
| FlatFeat/FFF | 23 |
| GCG | 5 |
| GFF | 24 |
| IG/Stanford | 1 |
| MSF | 15 |
| NBRF | 3 |
| PAUP/NEXUS | 17 |
| Phylip(Phylip4) | 12 |
| Phylip3.2 | 11 |
| PIR/CODATA | 14 |
| Plain/Raw | 13 |
| SCF | 21 |
| XML | 19 |
Default value is: Auto-detected [0]
Output Format
Output format name.
| Format Name | Value |
|---|---|
| EMBL | 4 |
| GenBank | 2 |
| Fasta(Pearson) | 8 |
| Clustal/ALN | 22 |
| ACEDB | 25 |
| DNAStrider | 6 |
| FlatFeat/FFF | 23 |
| GCG | 5 |
| GFF | 24 |
| IG/Stanford | 1 |
| MSF | 15 |
| NBRF | 3 |
| PAUP/NEXUS | 17 |
| Phylip(Phylip4) | 12 |
| Phylip3.2 | 11 |
| PIR/CODATA | 14 |
| Plain/Raw | 13 |
| Pretty | 18 |
| XML | 19 |
Default value is: EMBL [4]
Output Case
Change alphabet case for output sequences.
Default value is: No change [none]
Remove Gap Symbols
Remove gap symbols for output sequences.
| label | value |
|---|---|
| None | none |
| Symbol - | - |
| Symbol . | . |
Default value is: None [none]
Reverse-Complement of Input Sequencess
Reverse-complement of input sequences
Default value is: no [false]
Translate Symbols
Translate input symbol to output symbol.
Default value is:
Feature Selection
Feature to select
| Feature | Description |
|---|---|
| attenuator | |
| C_region | |
| CAAT_signal | |
| CDS | |
| conflict | |
| D-loop | |
| D_segment | |
| enhancer | |
| exon | |
| GC_signal | |
| gene | |
| iDNA | |
| intron | |
| J_segment | |
| LTR | |
| mat_peptide | |
| misc_binding | |
| misc_difference | |
| misc_feature | |
| misc_recomb | |
| misc_RNA | |
| misc_signal | |
| misc_structure | |
| modified_base | |
| mRNA | |
| N_region | |
| old_sequence | |
| polyA_signal | |
| polyA_site | |
| precursor_RNA | |
| prim_transcript | |
| primer_bind | |
| promoter | |
| protein_bind | |
| RBS | |
| repeat_region | |
| repeat_unit | |
| rep_origin | |
| rRNA | |
| S_region | |
| satellite | |
| scRNA | |
| sig_peptide | |
| snRNA | |
| source | |
| stem_loop | |
| STS | |
| TATA_signal | |
| terminator | |
| transit_peptide | |
| tRNA | |
| unsure | |
| V_region | |
| V_segment | |
| variation | |
| 3'clip | |
| 3'UTR | |
| 5'clip | |
| 5'UTR | |
| -10_signal | |
| -35_signal | |
| - |
Feature Handle
Handling selectd features - to remove or extract sequence of selected features.
| label | value |
|---|---|
| None | none |
| Remove sequence of selected features | remove |
| Extract sequence of selected features | extract |
Default value is: None [none]
Subrange
Subrange of sequence feature locations to extract. E.g., -1000..0 -- 1000 bases upstream to start of feature; 1..end1 -- the full range of the feature; end1..end100 -- from the end to 100 bases downstream of the feature; -100..end100 -- 100 bases upstream to 100 bases downstream; join-100..10,end1..end100 -- 100 bases upstream to 10 into joined with the end to 100 bases downstream.
Default value is:
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.
Email Address
If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).