WebProbe^TM

WebProbe helps users gain insight into their clusters by providing viewing tools that link consensus sequences, alignments, alignment analyses and external data sources like UniGene. The program assigns internal accession numbers to the clonelinks, clusters, contigs and consensus sequences produced in the clustering pipeline and these, as well as the original sequence accession numbers, may be used to query the viewer.

Clusters may have more than one possible consensus sequence, due to alternate splicing, chimeras or other isoforms of the gene represented by the cluster. Easily identifying and capturing variants of genes is critical to candidate discovery and the study of disease-related genes. StackPACK does not discard any information during the clustering process, and any variation is displayed in the WebProbe.

• Query by Accession Number
• Query by Sequence Accession Number
• Query by Cluster Accession Number
• Query by Contig Accession Number
• Query by Clonelink Accession Number
• Query by Consensus Accession Number
• Consensus and Alignment Views
• Consensus View
• Initial PHRAP Alignment View
• Alignment Analysis View
• Final CRAW Alignment View
• Obtain a summary report
• Search for possible alternate expression forms

• Enter the project name and owner, or use the "Search" option to filter the full project list.
• The search option allows the user to search the full project list for the relevant project, with all or part of the project name.
• StackPACK is not case-sensitive. Therefore, project names such as "UPPER" and "Upper" will be considered duplicates if they have the same owner.

• Enter the accession number of a sequence in the box provided to see the sequence and the cluster family it belongs to.
• Every sequence must have a unique accession number (per project) in order for all the data to be processed. If the original input file contained two or more sequences with the same accession number, the program will have only processed the first sequence. The other duplicate(s) will not be imported or processed regardless of its actual primary sequence data.

Example:

• Click the "View" button to retrieve the sequence information.
• The Sequence View is displayed.
• A window similar to the following is displayed with sequence information in the right panel and the full cluster family in the left panel.

• Annotation information supplied with the input file is provided in the description header. This information may indicate features of the sequence such as template (subclone), read orientation, length, etc. While the program will make every attempt to parse details from the input data, this is dependent on the exact format and content of your original sequences.
• If the sequence is part of a cluster, the entire cluster family tree is shown in the left panel, as in the example above.
• If the sequence is a singleton, only the sequence accession number is displayed in the left panel.
• Clicking on the "U" next to the sequence accession number in the cluster tree will query NCBI's Entrez for that sequence. This action will be taken regardless of whether or not the sequence accession number is a valid NCBI accession number.

• Within the Sequence View, the user may query the program for other entries in the same project.
• Query can be done by sequence accession number, clonelink accession number, cluster accession number, contig accession number or consensus accession number.
• To use, type in an accession number and click the 'View' button.

FAQ: Why are the fonts within WebProbe misaligned?
Answer:

• This may due to the browser font settings. The browser fonts should be set to use document specified fonts, including dynamic fonts.
• On Netscape it is set as follows: Edit; Preferences; Fonts.
• On IE it is set as follows: Tools; Internet Options; Accessibility; Formatting.

• Enter the project name and owner, or use the "Search" option to filter the full project list.
• The search option allows the user to search the full project list for the relevant project, with all or part of the project name.
• StackPACK is not case-sensitive. Therefore, project names such as "UPPER" and "Upper" will be considered duplicates if they have the same owner.

• Allows the user to query the viewer by cluster accession number.
• Enter the accession number of a cluster in the box provided to see the cluster consensus sequence(s) and the details of the full cluster family.

Example:

FAQ: How do I know a cluster's accession number?
Answer: During the clustering pipeline, the program assigns internal cluster numbers to each of the clusters produced, starting at cl1 (cluster 1).
To find all cluster accession numbers for a project:

• Go to stackPACK WebProjectManager.
• Request a summary report by clicking on the project name.
• StackPACK will provide you with a summary report listing the total number of clonelinks, clusters and singletons.
• • Clicking on the total number of multi-sequence clusters link takes the user to the list of cluster accession numbers in the project.
  • Clicking on the total number of linked clusters link takes the user to the list of linked cluster accession numbers in the project.

• Click the "View" button to retrieve the cluster information.
• The cluster Consensus View is displayed by default and shows all potential consensus sequences for all cluster contigs.
• This cluster Consensus View is also displayed when clicking on the icon next to the cluster accession number in the cluster tree. The text "All cluster Consensus Sequences" is displayed when holding the mouse over this icon.
• A window similar to the following is displayed, with cluster consensus sequence(s) in the right panel and the cluster family in the left panel.

• In every view of the cluster, the full cluster family is visually presented in a tree format. In this example, the clonelink accession number, ln5, is seen at the top of the tree, and the two constituent cluster accession numbers, cl8 and cl20 branch off from it. cl8 consists of one contig, ct8, and ct8 consists of one consensus, cn9. cn9 consists of three EST sequences, H64404, H64416 and H64428, that bracnch off from it.
• Clusters are created by the d2_cluster algorithm and subsequently may be split into one or more contigs by the PHRAP assembly algorithm due to its stricter methods. This gives rise to the contig accession number. PHRAP may also split off single sequences from the cluster formed by d2_cluster. These are referred to as PHRAP singletons. The cluster in this example has only one contig. (See stackPACK Conventions for further details).

Note: Very large clusters may not always be viewable due to browser limitations.

• Clicking on the clonelink accession number in the tree downloads a single FASTA-format file containing all sequences in the clonelink.
• Clicking on the cluster accession number in the tree downloads a single FASTA-format file containing all sequences in the cluster.
• Clicking on the contig accession number in the tree downloads a single FASTA-format file containing all sequences in the contig.
• Clicking on the consensus accession number in the tree downloads a single FASTA-format file containing all sequences in the consensus.
• Clicking on the icons next to the contig accession number gives the user access to the various stackPACK alignment and analysis views. Placing the mouse pointer over an icon will also bring up text describing the function of that icon.
• Clicking on the 'U' next to a sequence accession number in the tree will search NCBI's UniGene Homo sapiens database for the corresponding UniGene entry. This option appears regardless of whether or not the sequence accession number is a valid NCBI accession number.
• Clicking on any of the constituent EST or mRNA sequence accession numbers in the tree takes the user to that sequence view:

• This option allows the user to query the program for other entries in the same project.
• Query can be done by sequence accession number, clonelink accession number, cluster accession number, contig accession number or consensus accession number.
• To use, type in an accession number and click the 'View' button.

FAQ: How do I know if my project contains clusters with alternate expression forms?
Answer: During the clustering pipeline, the program looks for subalignments that might represent alternate expression forms.

To find all clusters in a project with alternate expression forms:

1. Go to stackPACK WebProbe by clicking on WebProbe in the menu bar.
2. Enter the project name and owner, or use the search option to search for the relevant project.
3. Request an Alternates Report by clicking on the "Alternates_Search" button.
4. Click "View".

StackPACK will provide you with a list of contigs that contain potential alternate expression forms.

• Enter the project name and owner, or use the "Search" option to filter the full project list.
• The search option allows the user to search the full project list for the relevant project, with all or part of the project name.
• StackPACK is not case-sensitive. Therefore, project names such as "UPPER" and "Upper" will be considered duplicates if they have the same owner.

• Allows the user to query the viewer by contig accession number.
• Enter the accession number of a contig in the box provided to see the cluster consensus sequence(s) and the details of the full cluster family.

Example:

• Click the "View" button to retrieve the cluster information.
• The contig Consensus View is displayed by default.
• This contig Consensus View corresponds to the PHRAP Consensus Sequence, and is also displayed when clicking on the first icon from the left next to the contig accession number in the cluster tree. The text "PHRAP Consensus Sequence" is displayed when holding the mouse over this icon.
• A window similar to the following is displayed, with contig consensus sequence in the right panel and the cluster family in the left panel.

• In every view of the cluster, the full cluster family is visually presented in a tree format. In this example, the clonelink accession number, ln4, is seen at the top of the tree, and the two constituent cluster accession numbers, cl7 and cl19 branch off from it. cl7 consists of one contig, ct7, and ct7 consists of one consensus, cn8. cn8 consists of two EST sequences, H64403 and H64415 that bracnch off from it.
• Clusters are created by the d2_cluster algorithm and subsequently may be split into one or more contigs by the PHRAP assembly algorithm due to its stricter methods. This gives rise to the contig accession number, ct1. PHRAP may also split off single sequences from the cluster formed by d2_cluster. These are referred to as PHRAP singletons. The cluster in this example has only one contig. (See stackPACK Conventions for further details).

Note: Very large clusters may not always be viewable due to browser limitations.

• Clicking on the clonelink accession number in the tree downloads a single FASTA-format file containing all sequences in the clonelink.
• Clicking on the cluster accession number in the tree downloads a single FASTA-format file containing all sequences in the cluster.
• Clicking on the contig accession number in the tree downloads a single FASTA-format file containing all sequences in the contig.
• Clicking on the consensus accession number in the tree downloads a single FASTA-format file containing all sequences in the consensus.
• Clicking on the icons next to the contig accession number gives the user access to the various stackPACK alignment and analysis views. Placing the mouse pointer over an icon will also bring up text describing the function of that icon.
• Clicking on the 'U' next to a sequence accession number in the tree will search NCBI's UniGene Homo sapiens database for the corresponding UniGene entry. This option appears regardless of whether or not the sequence accession number is a valid NCBI accession number.
• Clicking on any of the constituent EST or mRNA sequence accession numbers in the tree takes the user to that sequence view:

• This option allows the user to query the program for other entries in the same project.
• Query can be done by sequence accession number, clonelink accession number, cluster accession number, contig accession number or consensus accession number.
• To use, type in an accession number and click the 'View' button.

• Enter the project name and owner, or use the "Search" option to filter the full project list.
• The search option allows the user to search the full project list for the relevant project, with all or part of the project name.
• StackPACK is not case-sensitive. Therefore, project names such as "UPPER" and "Upper" will be considered duplicates if they have the same owner.

• Allows the user to query the viewer by clonelink accession number.
• Enter the accession number of a clonelink in the box provided to see the clonelink consensus sequence and the details of the full cluster family.

Example:

FAQ: How do I know if my project has any clonelinked clusters?
Where do I find clonelink accession numbers for my project?
Answer: During the clustering pipeline, the program assigns internal cluster numbers to each of the clonelinks produced, starting at ln1 (link 1).
To find all cluster accession numbers for a project:

• Go to stackPACK WebProjectManager.
• Request a summary report by clicking on the project name.
• StackPACK will provide you with a summary report listing the total number of clonelinks, clusters and singletons.
• Clicking on the total number of multi-sequence clusters link takes the user to the list of cluster accession numbers in the project.
• Clicking on the total number of linked clusters link takes the user to the list of linked cluster accession numbers in the project.

• Click here to retrieve the clonelink information.
• The clonelink consensus sequence is displayed in the main panel with the full cluster family in the left panel, as seen below.

• The clonelink is presented in a tree format with the clonelink number (ln4) at the top and the constituent clusters (cl7 and cl19) with their respective contigs, consensus sequences and sequences (EST or mRNA) branching off from each.
• Clone linking is performed only if clone ID information is provided with the input file in a format recognized by stackPACK.
• For clusters and singletons to clonelink, they must share clone ID information. The redundancy of clone ID information required to make a link is specified in the stackPACK configuration file(s).
• The clonelink consensus sequence is created by concatenating the primary consensus sequences from each of the constituent clusters, separating each with a linker region of 20 consecutive Xs.
• If a clonelink consists of contigs which have alternate consensus sequences, only the cluster primary consensus sequence(s) will be used to generate the clonelink. The user does however have access to the alternate consensus sequences when querying the viewer with the cluster accession number.
• If a clonelink consists of clusters which have mutiple contigs, the primary consensus sequences of all contigs will be used to generate the clonelink.

• Clicking on the clonelink accession number in the tree downloads a single FASTA-format file containing all sequences in the clonelink.
• Clicking on the cluster accession number in the tree downloads a single FASTA-format file containing all sequences in the cluster.
• Clicking on the contig accession number in the tree downloads a single FASTA-format file containing all sequences in the contig.
• Clicking on the consensus accession number in the tree downloads a single FASTA-format file containing all sequences in the consensus.
• Clicking on the icons next to the contig accession number gives the user access to the various stackPACK alignment and analysis views. Placing the mouse pointer over an icon will also bring up text describing the function of that icon.
• Clicking on the 'U' next to a sequence accession number in the tree will search NCBI's UniGene Homo sapiens database for the corresponding UniGene entry. This option appears regardless of whether or not the sequence accession number is a valid NCBI accession number.
• Clicking on any of the constituent EST or mRNA sequence accession numbers in the tree takes the user to that sequence view.

Note: Very large clonelinks may not always be viewable due to browser limitations.

• This option allows the user to query the program for other entries in the same project.
• Query can be done by sequence accession number, clonelink accession number, cluster accession number, contig accession number or consensus accession number.
• To use, type in an accession number and click the 'View' button.

• Enter the project name and owner, or use the "Search" option to filter the full project list.
• The search option allows the user to search the full project list for the relevant project, with all or part of the project name.
• StackPACK is not case-sensitive. Therefore, project names such as "UPPER" and "Upper" will be considered duplicates if they have the same owner.

• Allows the user to query the viewer by consensus accession number.
• Enter the consensus accession number of the contig of interest in the box provided to see the consensus sequence and the details of the full cluster family.

Example:

FAQ: How do I know a consensus' accession number?
Answer:

• During the clustering process, stackPACK assigns internal consensus numbers to each of the consensus sequences produced, starting at cn1 (consensus 1).
• To find the accession number for a particular consensus sequence:
1. Go to stackPACK WebProbe.
2. Enter the project name and owner, or use the search option to search for the relevant project.
3. Enter the cluster accession number to which the contig in question belongs to in the box provided.
4. Click "View".
• The consensus accession number can always be found as part of the cluster family tree on the left panel of the view.
• Alternatively, consensus accession numbers can be obtained from the comma-separated values formatted report. Please refer to WebReport for further details on the reporting functions.

• Click the "View" button to retrieve the consensus information.
• The Final Consensus View is displayed by default
• The Final Consensus Sequence, and is also displayed when clicking on the first icon from the left next to the consensus accession number in the cluster tree. The text "Final Conensus Sequence" is displayed when holding the mouse over this icon.
• A window similar to the following is displayed, with the final consensus sequence in the right panel and the cluster family in the left panel:

• The full cluster family is visually presented in a tree format. In this example, the clonelink, ln11, is at the top of the tree. The constituent cluster (cl16) with its contig, consensus sequences and EST sequences branch off from it.

Note: Very large clusters may not always be viewable due to browser limitations.

• Clicking on the clonelink accession number in the tree downloads a single FASTA-format file containing all sequences in the clonelink.
• Clicking on the cluster accession number in the tree downloads a single FASTA-format file containing all sequences in the cluster.
• Clicking on the contig accession number in the tree downloads a single FASTA-format file containing all sequences in the contigs.
• Clicking on the consensus accession number in the tree downloads a single FASTA-format file containing all sequences in the consensus.
• Clicking on the icons next to the contig accession number gives the user access to the various stackPACK alignment and analysis views.
• Clicking on the 'U' next to a sequence accession number in the tree will search NCBI's UniGene Homo sapiens database for the corresponding UniGene entry. This option appears regardless of whether or not the sequence accession number is a valid NCBI accession number.
• Clicking on any of the constituent EST or mRNA sequence accession numbers in the tree takes the user to that sequence view.

There are four different consensus views within stackPACK: The "PHRAP Consensus Sequence View", the "Final Consensus Sequence View", the "All Final Consensus Sequence(s) View" and the "Clonelink Consensus Sequence View". These views are displayed upon clicking the appropriate icon within the cluster family tree.

If the cluster or contig in question has more than one consensus sequence, the sequences are displayed ranking from best to worst in the All Final Consensus Sequence(s) View. Consensus sequence positions where all contributing sequences are masked (i.e,. are 'x') are calculated as "n". If a consensus sequence has more than 10 "n" bases in a row due to the underlying data being masked, the program will truncate these regions of the consensus to 10 "n" bases only.

In cases where sequence data have been imported without quality scores, the PHRAP consensus sequence and PHRAP alignment will always be in lower case due to the default quality parameter. If users wish to use case as an an indicator of quality, the older PHRAP version, PHRAP v 0.960731 should be used. Please refer to section 6, Expert Configuration, of the Command Line manual for details. The newer version of PHRAP, PHRAP v 0.960731, is used by default within stackPACK.

• The longest consensus sequence is ranked best.
• If consensus sequences are the same length, the program compares number of constituent sequences (ESTs or mRNAs) next.
• If both length and number of constituent sequences are equal, the prgram then ranks the consensus sequences by the number of good bases (i.e., A, T, C, or G).

Note: If PHRAP is unable to align the sequences clustered together by d2_cluster and thus unable to create a contig for that particular cluster, there will be no alignment or consensus sequence for that cluster. Only the EST or mRNA sequence view is accessible.

In order to take advantage of the benefits of looser clustering, the clusters generated are subsequently aligned and analyzed in the clustering pipeline process. The PHRAP algorithm is used for the assembly and initial alignment phase.

PHRAP assembles and aligns the sequences grouped together by d2_cluster. Because the method used by PHRAP is more stringent and less tolerant of noisy EST or single-pass sequences, it may not be able to align all the sequences from a single cluster into one contig. Therefore, PHRAP may sometimes split a cluster into multiple contigs and/or may even split out particularly distinct sequences as PHRAP singletons.

The PHRAP Alignment View represents the raw alignment, (before it has been analyzed), and displays a single alignment for the whole contig in question. Any PHRAP singletons created will not show as part of the alignments.

In the following example contig 10 consists of 7 ESTs contributing to 1 consensus sequences (viewable in the cluster Consensus View). Only one PHRAP alignment is generated regardless of the number of alternate sequences.

• StackPACK is able to output the PHRAP alignments into MSF, ClustalW and ACE formats from WebReport for further searching, editing and use in other programs. Long sequence accession numbers may push out the alignment output for that sequence, and may be truncated in external programs such as ClustalW.
• PHRAP has a limit of 64K bases for each sequence. If a cluster contains sequences that exceed this limit, a consensus sequence will not be generated for this cluster. Please refer to section 6 of the Command Line manual, Expert Configuration, for details on how to overcome this.

Note: Very long sequences such as long mRNAs may wrap in the Alignment Views due to browser limitations.

• Plain Text
• This option displays all the bases in plain, black ascii text.
• All bases are displayed.
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.
• Coloured Bases
• This option displays each nucleotide base in a different color.
• All bases are displayed.
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.
• Differences Only
• This option displays only those bases in the constituent sequences that differ from the consensus sequence.
• Bases that are the same as the consensus sequence are represented by a single dot (".").
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.
• Highlighted Differences
• This option highlights those bases in the constituent sequences that differ from the consensus sequence with a " ^ " placed below the differing base.
• All bases are displayed in plain ascii text.
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.

FAQ: Why are some of my sequences missing from the contigs or assembly analysis?
Answer: When PHRAP attempts to assemble the sequences brought together by d2_cluster, it may not only split the loosely clustered group into multiple contigs, but it may also separate particularly divergent sequences that don't align well to any of the contigs as singletons. We refer to these sequences as PHRAP singletons.

The assembly analysis step ONLY analyzes contigs and therefore final consensus sequences are only generated from contigs. As a result, PHRAP singletons, while displayed with a cluster in the cluster tree on the left side of the screen, are not used in the assembly analysis step and therefore do not appear in assembly analysis or CRAW alignment views and are not included in final consensus generation.

CRAW is employed to create sub-assemblies, identify potential alternate expression forms for each contig and provide a simple means to view clusters.

CRAW analyzes the alignment produced by PHRAP and, in conjunction with the remainder of the Analysis step (stack_Analysis), updates the consensus sequence to produce the CRAW Alignment View. If subalignments are identified by CRAW, a separate alignment is shown for each subalignment.

• The alternate consensus sequences with their aligned constituent sequences are displayed ranking from best to worst in the CRAW Alignment View. This matches the order found in the "All Final Consensus Sequence(s) View".
• If the constituent sequence contains a masked region, noted with 'x' in the sequence, the masked region will be displayed in the CRAW Alignment View. If all the constituent sequences in a particular region of the CRAW alignment are masked, the resultant consensus will be noted with lower case 'n'.
• The name of each constituent sequence is provided to the left as well as the right of the sequence.
• If annotative information, such as library name, has been imported with the sequence data it will be displayed in the CRAW Alignment View on the right after the sequence accession number. This example did not have any annotations.
• Each CRAW alignment may be exported in MSF and CLUSTAL formats from WebReport for further editing, formatting and use in other programs. Long sequence accession numbers may push out the alignment output for that sequence, and may be truncated in external programs such as ClustalW.

Note: Very long sequences such as long mRNAs may wrap in the Alignment Views due to browser limitations.

• Plain Text
• This option displays all the bases in plain, black ascii text.
• All bases are displayed.
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.
• Colored Bases
• This option displays each nucleotide base in a different color.
• All bases are displayed.
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.
• Differences Only
• This option displays only those bases in the constituent sequences that differ from the consensus sequence.
• Bases that are the same as the consensus sequence are represented by a single dot (".").
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.
• Highlighted Differences
• This option highlights those bases in the constituent sequences that differ from the consensus sequence with a " ^ " placed below the differing base.
• All bases are displayed in plain ascii text.
• Gaps are represented by dashes in both the consensus sequence and the constituent sequences.

FAQ: Why do some of the contigs not contain CRAW alignments?
Answer:

• This may happen with particularly large contigs, when the CRAW output is too large to be imported into the database.
• In this event, neither the CRAW Alignment nor the Alignment Analysis view will be available.

Clusters may have more than one consensus sequence, due to alternate expression forms, chimeras or other isoforms of the gene represented by the cluster. Alignment Analysis View provides a single view of the entire cluster to highlight the variation that may occur.

CRAW locates subalignments within the alignment generated by PHRAP. These subalignments are represented by different numbers in the Alignment Analysis View and correspond to putative alternate expression forms. Generally, the primary alignment (subalignment with the largest number of members) is thus represented by 1, the first alternate subalignment by 2, and so on.

Example:

• In order for the whole sequence to be displayed in one page, the CRAW algorithm, employed in Alignment Analysis, condenses the entire sequence length into 60 characters. Hence one character will represent a certain number of bases depending on the total sequence length. In this example one position equals 43 bases. This statistic can be found at the top of each Alignment Analysis View.
• In this example:
• The primary alignment is due to the following ESTs: X53742, D58709, R70585, T46970
• The secondary alignment is due to the following ESTs: AA142940, AI88632, AI130996, AA642240, AA778132, AA614616, AA412148. AA130067, R25317, AI084677.
• If imported with the original sequences, annotation such as the library names and clone IDs will be displayed to the right of each sequence accession number.
• Clicking on the constituent sequence accession numbers, either in the tree or in the annotation, takes the user to the corresponding Sequence View.

FAQ: Why do some of the contigs not contain Alignment Analyses?
Answer:

• This may happen with particularly large contigs, when the CRAW output is too large to be imported into the database.
• In this event, neither the CRAW Alignment nor the Alignment Analysis view will be available.
• All the CRAW logs for a particular project may be extracted from WebReport or from command line with the stack_ReportAlignment.py report. Please refer to section 5 of the command line manual, Exporting Data from the Command Line, for further details.

• Enter the project name and owner, or use the "Search" option to filter the full project list.
• The search option allows the user to search the full project list for the relevant project, with all or part of the project name.
• Note: StackPACK is case-sensitive. Please be consistent when using upper or lower case for project names.

• Click here for a summary report of the specified project.
• A window similar to the following is displayed:

• Linked Clusters: Singletons and multi-sequence clusters joined by virtue of shared cloneID.
  • Total number of clonelinks.
  • Number of sequence found in linked clusters.
  • Number of singletons found in linked clusters.
  • Number of multi-sequence clusters found in linked clusters.
• Multi-sequence Clusters: Sequences grouped together into clusters.
  • Total number of multi-sequence clusters.
  • Number of sequences in multi-sequence clusters.
  • Number of multi-sequence clusters found in linked clusters.
  • Number of multi-sequence clusters not found in linked clusters.
• Singletons: Sequences which could not be grouped into clusters with other sequences.
  • Total number of singletons
  • Sequences in Singletons - always n/a.
  • Number of singletons found in linked clusters.
  • Number of singletons not found in linked clusters.

Note: Clusters that have been deprecated due to the incremental addition of sequence data to existing clusters will not be listed in the summary report. These clusters can be viewed in WebProbe.

• Clicking on the total number of linked clusters link (22 in the above example) takes the user to a list of total clonelinks in the specified project.
  • Clicking on a clonelink accession number takes the user to that clonelink consensus view.
• Clicking on the total number of multi-sequence clusters link (268 in the above example) takes the user to a list of total multi-sequence clusters in the specified project.
• Clicking on a cluster accession number takes the user to the cluster consensus view. If the cluster contains more than one contig, all consensus sequences from all contigs will be concatenated in this single view.
• Clicking on the total number of singletons link (0 in the above example) takes the user to a list of total singletons in the specified project.
• Clicking on a singleton accession number takes the user to the singleton sequence.

Long summary lists will be split into multiple pages. To view the following page, simply click the "Next" link at the bottom of the screen. In cases of very long lists, click on the "(+10)" link in order to move 10 pages forward.

• Enter the project name and owner, or use the "Search" option to filter the full project list.
• The search option allows the user to search the full project list for the relevant project, with all or part of the project name.
• Note: StackPACK is case-sensitive. Please be consistent when using upper or lower case for project names.

• Click here for a list of contigs with potential alternate expression forms.
• A window similar to the following is displayed:



• Clicking on the contig accession numbers displays the cluster contig's Alignment Analysis view.