LALIGN (Nucleotide Alignment)

Introduction

LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or DNA sequences

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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
BLOSUM50 BL50
BLOSUM62 BL62
BLASTP62 BP62
BLOSUM80 BL80
PAM120 P120
PAM250 P250
MDM10 M10
MDM20 M20
MDM40 M40

Default value is: BLOSUM50 [BL50]

Additional information

Gap Open Penalty

Pairwise alignment score for the first residue in a gap.

Default value is: -12

Additional information

Gap Extend Penalty

Pairwise alignment score for each additional residue in a gap.

Default value is: -4

Additional information

Expectation Threshold

Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.

Default value is: 10.0

Output formats

Pairwise sequences format

Value Description
0 Uses ":", ".", " " for identities, conservative replacements, and non-conservative replacements, respectively
1 Uses " ","x", and "X" for identities, conservative replacements, and non-conservative replacements, respectively
2 Does not show the second sequence, but uses the second alignment line to display matches with a "." for identity, or with the mismatched residue for mismatches. MARKX=3 is useful for aligning large numbers of similar sequences

Default value is: MARKX 0 [0]

Visual Output

Generates a visual output

Default value is: yes [true]

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).

References

A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600