EMBOSS Needle (Protein Alignment)
Introduction
EMBOSS Needle reads two input sequences and writes their optimal global sequence alignment to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length.
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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
First Input Sequence
A free text (raw) list of sequences is simply a block of characters representing several DNA/RNA or Protein sequences. A sequence 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.
First Sequence File Upload
A file containing valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. Word processors 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.
Second Input Sequence
A free text (raw) list of sequences is simply a block of characters representing several DNA/RNA or Protein sequences. A sequence 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.
Second Sequence File Upload
A file containing valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. Word processors 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.
Step 2 - Set alignment options
Matrix
Default substitution scoring matrices.
| Matrix Name | Abbreviation |
|---|---|
| BLOSUM30 | EBLOSUM30 |
| BLOSUM35 | EBLOSUM35 |
| BLOSUM40 | EBLOSUM40 |
| BLOSUM45 | EBLOSUM45 |
| BLOSUM50 | EBLOSUM50 |
| BLOSUM55 | EBLOSUM55 |
| BLOSUM60 | EBLOSUM60 |
| BLOSUM62 | EBLOSUM62 |
| BLOSUM65 | EBLOSUM65 |
| BLOSUM70 | EBLOSUM70 |
| BLOSUM75 | EBLOSUM75 |
| BLOSUM80 | EBLOSUM80 |
| BLOSUM85 | EBLOSUM85 |
| BLOSUM90 | EBLOSUM90 |
| BLOSUM Clustered | EBLOSUMN |
| PAM 10 | EPAM10 |
| PAM 20 | EPAM20 |
| PAM 30 | EPAM30 |
| PAM 40 | EPAM40 |
| PAM 50 | EPAM50 |
| PAM 60 | EPAM60 |
| PAM 70 | EPAM70 |
| PAM 80 | EPAM80 |
| PAM 90 | EPAM90 |
| PAM 100 | EPAM100 |
| PAM 110 | EPAM110 |
| PAM 120 | EPAM120 |
| PAM 130 | EPAM130 |
| PAM 140 | EPAM140 |
| PAM 150 | EPAM150 |
| PAM 160 | EPAM160 |
| PAM 170 | EPAM170 |
| PAM 180 | EPAM180 |
| PAM 190 | EPAM190 |
| PAM 200 | EPAM200 |
| PAM 210 | EPAM210 |
| PAM 220 | EPAM220 |
| PAM 230 | EPAM230 |
| PAM 240 | EPAM240 |
| PAM 250 | EPAM250 |
| PAM 260 | EPAM260 |
| PAM 270 | EPAM270 |
| PAM 280 | EPAM280 |
| PAM 290 | EPAM290 |
| PAM 300 | EPAM300 |
| PAM 310 | EPAM310 |
| PAM 320 | EPAM320 |
| PAM 330 | EPAM330 |
| PAM 340 | EPAM340 |
| PAM 350 | EPAM350 |
| PAM 360 | EPAM360 |
| PAM 370 | EPAM370 |
| PAM 380 | EPAM380 |
| PAM 390 | EPAM390 |
| PAM 400 | EPAM400 |
| PAM 410 | EPAM410 |
| PAM 420 | EPAM420 |
| PAM 430 | EPAM430 |
| PAM 440 | EPAM440 |
| PAM 450 | EPAM450 |
| PAM 460 | EPAM460 |
| PAM 470 | EPAM470 |
| PAM 480 | EPAM480 |
| PAM 490 | EPAM490 |
| PAM 500 | EPAM500 |
Default value is: BLOSUM62 [EBLOSUM62]
- Additional information
Gap Open Penalty
Pairwise alignment score for the first residue in a gap.
Default value is: 10
- Additional information
Gap Extend Penalty
Pairwise alignment score for each additional residue in a gap.
Default value is: 0.5
- Additional information
Output formats
Pairwise sequences format
| Value | Description |
|---|---|
| pair | The sequences have the markup line between them |
| markx0 | This is the standard default output format used by Bill Pearson's suite of FASTA programs |
| markx1 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which identities are not marked. Instead conservative replacements are denoted by 'x' and non-conservative substitutions by 'X' |
| markx2 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the residues in the second sequence are only shown if they are different from the first |
| markx3 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format. These can be used to build a primitive multiple alignment |
| markx10 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format and the sequence length, alignment start and stop information is given in lines starting with a ';' character just after the title line for each sequence. It is intended to be easily parsed by other programs |
| srspair | This is very similar in style to pair format |
| score | This does not display the sequence alignment. It shows only the names of the sequences, the length of the alignment and the score |
Default value is: pair
End Gap Penalty
Apply end gap penalty
Default value is: false
End Gap Open Penalty
Score taken away when an end gap is created.
Default value is: 10
- Additional information
End Gap Extend Penalty
Penalty is added to the end gap penalty for each base or residue in the end gap. This is how long end gaps are penalized.
Default value is: 0.5
- Additional information
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).