Help Pages
Feature Annotations
The full genome sequence has been annotated with features including:
Gene
DescriptionGenes form the core of the Methanosarcina acetivorans annotation. As described in detail previously, genes are called by a manual process based on the results of automated analyses tools.
Genes that could not be conclusively identified were assigned one of the following standard gene names:
- predicted protein -a gene predicted automatically by Glimmer (see below) that had no similarity to the public protein or nucleotide databases (see BlastX and BlastN in the Feature Types sections below for a description of the thresholds used for searching).
- conserved hypothetical protein - This feature was selected when there was a set of blast hits for a gene consisting of unknown or hypothetical proteins, some of which spanned at least 80% of the length of the ORF. It could also be used when a Hmmer feature was present and indicated an unknown family protein (UFP) or a domain (e.g. PUA or PAS domain) found in uncharacterized proteins.
- hypothetical protein (multi-domain) - This feature was selected when partial Blastx features of different known or unknown proteins spanned different regions of the Glimmer ORF. These genes were marked for further review.
- hypothetical protein (inconsistent evidence) - This feature was selected when there was conflicting identities among the Blastx features all or some of which spanned at least 80% of the length of the ORF. These genes were marked for further review.
- pseudogene - This feature was selected when truncated glimmer ORFs were spanned by one or several blastx features of known or unknown proteins.
- hypothetical protein (not yet displayed as an identifying feature in Calhoun) - This feature was used when a Hmmer feature pointing to an uncharacterized family protein and no Blastx features were present. It was also used when the glimmer ORF had homology to a portion or domain of blastx features. The blastx features spanned least 80% of the ORF and did not represent the whole protein but a portion of it (230-400 amino acids of a protein that is 500aa long for example). These genes were marked for further review.
GENE Feature Attributes
The figure below is a screen shot of the Methanosarcina acetivorans website showing feature details for an annotated pyruvate kinase gene.
The attributes for a GENE feature are:
- Locus A unique public identifier for the gene. Locus Ids are assigned to each gene in order starting from base pair 1. In this screen shot, the gene has not been assigned a Locus.
- Gene Name The name of the gene product. These were assigned as described above. Where EC Numbers were determined, the gene name was selected to be the "Official Name" for the Enzyme.
- Symbol The gene symbol. Where possible these have been selected to follow the literature for Methanogens. In the absence of a convention in Methanogens, the E. coli convention was preferred.
- EC Number The identifier assigned by the Enzyme Commission (see http://ca.expasy.org/enzyme/) to each type of characterized enzyme. Where EC Numbers were determined, the gene name was selected to be the "Official Name" for the Enzyme.
- Functional Role The functional role for the gene product as classified according to the TIGR Classification Scheme.
- Sequence The name of the sequence on which the gene has been called. In the example shown above, the gene was called after the contigs making up the assembly were combined into a single genome sequence.
- Start The start position of the gene on the sequence. Start is always less than stop.
- Stop The stop position of the gene on the sequence. Stop is always greater than start.
- Strand The strand on which the gene was called (+ or -).
- Subtype The feature type. GENE for all gene calls.
- Last Reviewed The date this gene was last modified.
- TIGR Gene Name TIGR performed an automated analysis on the set of predicted proteins. This field contains the name automatically assigned by TIGR's analysis.
- TIGR Gene Role TIGR performed an automated analysis on the set of predicted proteins. This field contains the TIGRFAM role automatically assigned by TIGR's analysis.
- Kegg Map by EC# - A list of Kegg Maps (http://www.genome.ad.jp/kegg/) to which the EC number assigned to this gene have been mapped. These mappings should not be relied upon as a classification of the function of the gene. Rather they have been generated as a convenience to allow users to quick determine what pathways a particular enzyme might be operating within.
Glimmer
Description
Features of type Glimmer, are ORFs that have been predicted by the microbial gene finder Glimmer version 2.0 (http://www.cs.jhu.edu/labs/compbio/glimmer.html). Glimmer uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Glimmer version 2.0 was used.
As described above, Glimmer was the starting point for all manually annotated gene calls and in the majority of cases, manually called genes were given the same location as the corresponding Glimmer ORF. However, it must be kept in mind that Glimmer is known to be innaccurate in predicting the exact start position of genes. This is in part due to the large number of potential start codons in bacterial genomes. In most cases Glimmer will call the longest gene consistent with the codon statistics in the open reading frame.
From , Glimmer finds between 97-98% of genes as compared to published annotations. When accuracy is determined by looking for genes with significant database matches, Glimmer finds greater than 99% of these genes (see http://www.cs.jhu.edu/labs/compbio/glimmer.html). Thus Glimmer is very sensitive in its ability to find genes and the absence of a glimmer feature in a sequence region is a strong indication that no gene is present. These results were borne out with the Methanosarcina annotation in that less than a dozen regions were seen to have sequence similarity to a gene in NR (see BlastX below) without a corresponding Glimmer feature overlapping the region.
In contrast, the number of false positives predicted by Glimmer is difficult to determine since the asserting that an ORF is not a gene is essentially impossible. However, based on other published annotations, it is apparent that Glimmer calls many more false positives for short genes. Thus, to limit this problem, we have set a 200 bp limit on the size of a glimmer orf that will be considered as being a potential gene. However, our website does include glimmer features shorter than this length.
GLIMMER Feature Attributes
The above figure is a screen shot of the Methanosarcina acetivorans website showing feature details for a feature of type GLIMMER.
The attributes for a GLIMMER feature are:
- Glimmer ORF The unique name assigned to the predicted gene.
- Sequence The name of the sequence on which this feature has been called. In the example shown above, the gene was called before the contigs making up the assembly where combined into a single genome sequence.
- Start The start position of the feature on the sequence. Start is always less than stop.
- Stop The stop position of the feature on the sequence. Stop is always greater than start.
- Length Length of the predicted feature.
- Strand The strand on which the feature was called (+ or -).
- Subtype The feature type.
- Score The probability that this ORF is a gene as assigned to this prediction by Glimmer. Only features with a score of at least 90 are included in the Methanosarcina acetivorans annotation.
- Frame The reading frame of this feature
- Notation notes overlapping predicted ORFs
BlastX
Description
Features of type BLASTX correspond to the results of searching the complete genome of Methanosarcina acetivorans against the public non-redundant protein database (nr) using the Blast . The genome was initially searched against a version of the database dated August 11,2000 and subsequently searched again against a version of the database dated February 14, 2001. Release 2.0 of the NCBI Blast implementation was used.
The genome was searched against the database in 50KB windows overlapping each other by 10KB. The genome was not complexity filtered. Only blast hits with an "Expected value" less than 1e-5 were annotated on the genome.
Where redundant sequences were merged into a single nr entry, only the first member of the redundant set was annotated on the genome.
BLASTX Feature Attributes
The figure below is a screen shot of the Methanosarcina acetivorans website showing feature details for a feature of type BLASTX.
The attributes for a BLASTX features are:
- BlastX Hit The name of the hit protein as displayed in the nr fasta file
- Species Name The species corresponding to the hit sequence
- Score The score of the alignment
- Expected The probability of producing this alignment by chance
- %Identities The percentage of identities between the hit protein and the translated Methanosarcina acetivorans sequence
- Start The nucleotide start position of the feature on the sequence. Start is always less than stop
- Stop The nucleotide stop position of the feature on the sequence. Stop is always greater than start
- Length The length in nucleotides of the alignment on the Methanosarcina acetivorans sequence
- Strand The strand on which the feature was called (+ or -)
- Hit Start The amino acid start position within the hit sequence for this alignment
- Hit Stop - The amino acid stop position within the hit sequence for this alignment
- Query Sequence - The name of the sequence on which this feature has been called. In the example shown above, the gene was called after the contigs making up the assembly where combined into a single genome sequence
- Taxid The NCBI taxonomy ID for the hit sequence
- Identities The number of identities in the alignment reported by Blast
- Gaps The number of gaps in the alignment reported by Blast
- Positives The number of positive matches in the alignment reported by Blast
- Alignment The alignment for this feature
- GI - The gi number for this hit sequence.
- Blastdb The name of the blast database searched to generate this hit
- Rank Order For every gene, each of the top 20 overlapping blast hit is ranked according to its score with respect to other overlapping blast hits. A rank of 1 indicates the highest scoring blast hit for a particular gene.
- Subtype The type of this feature
BlastN
Features of type BLASTN correspond to the results of searching the complete genome of Methanosarcina acetivorans against the public non-redundant nucleotide database (nr) using the Blast . The genome was initially searched against a version of the database dated August 16,2000 and subsequently searched again against a version of the database dated February 14, 2001. Release 2.0 of the NCBI Blast implementation was used.
The genome was searched against the database in 50KB windows overlapping each other by 10KB. The genome was not complexity filtered. Only blast hits with an "Expected value" less than 1e-5 were annotated on the genome.
Where redundant sequences were merged into a single nr entry, only the first member of the redundant set was annotated on the genome.
BLASTN Feature Attributes
BLASTN feature attributes are identical to BLASTX feature attributes described in the previous section with the following exception: Hit Start and Hit Stop are defined in terms of nucleotide position on the hit sequence.
Hmmer
Description
Features of type HMMER correspond to the output of the HMMER program ( http://hmmer.wustl.edu/). HMMER is a tool for analyzing amino acid sequences to determine if they are evolutionarily related to a protein family or domain. Proteins from different organisms that perform the same function show differing degrees of sequence conservation in different regions of their sequences. A Hidden Markov Model (HMM) is a statisitical model that can be used to represents a protein family and can capture the fact that certain amino acid positions are well conserved and others are not.
We used HMMER v.2.1.2 to search against version 5.5 of Pfam (http://www.sanger.ac.uk/Software/Pfam/index.shtml) before performing our manual annotation. Since then we have reanalyzed the sequence using version 6.3 of Pfam and version 1.0 of TIGRFAM and have reviewed genes that have new results.
HMMER assigns a score to each hit it detects. Both Pfam and TIGRFAM include cutoff scores that can be used to automatically determine whether a hit is significant. The hits we include are ones that have a score greater than or equal to the 'gathering cutoff' for Pfam and the 'trusted cutoff' for TIGRFAM. These cutoffs are provided by the curators of these HMM's and are set so that when searching all known proteins using an HMM and using the score cutoff, only proteins that determined by the curators to be members of that protein family are retrieved.
Interpretation of HMMER hits depends on the nature of the sequence family that is hit. There are three main types of protein families that are contained in Pfam and TIGRFAM:
The first, and most useful, is a protein family that contains genes that all perform the same biological function. In many cases protein families of this type correspond to a distinct EC number. Hits to this type of protein family can generally be used to name the gene in question. An example is PF00120, the Glutamine synthetase family, which corresponds to EC:6.3.1.2.
The second type of family is a so-called 'superfamily' which includes two or more related but distinct proteins. A hit to this kind of protein family can be used to confirm an identification of one of the proteins in the superfamily, but in the absence of other evidence can only be used to identify a gene as a member of the superfamily. An example if PF01569, the PAP2 superfamily, which contains genes in EC:3.1.3.2, EC:3.1.3.9 and EC:3.1.3.27.
The third type of family is a protein domain, which is a portion of a protein that is conserved but can be found in more than one protein. Again, this can be used to confirm an identification made by other means but is typically not useful as the sole evidence for identifying a gene. An example is PF02310, the B12 binding domain, which is present in several different enzymes.
The identifications detailed in the paragraphs above are reasonable when the similarity identified by HMMER represents the full length of the HMM, and when the region of similarity in the ORF either covers most of the ORF, or the region covered is similar to the other members of the family. Another situation that can make identification more difficult is when the similarity is split into two regions in the same ORF, meaning that there is significant inserted sequence in the middle of the region that is not present in other members of the family. Lastly, if a gene contains hits to more than one protein family, the types and sources of those families needs to be reviewed to determine the correct call.
The primary data reported for a HMMER hit are a score, an expected value, and an alignment. The score is a log (base 2) odds ratio between the probability that the HMM generated the sequence and that the sequence was generated by a null (random) model. The expected value is a calculation of the probability that this match could have occurred by chance. The alignment is the optimum alignment between the query sequence and the HMM consensus sequence. The consensus is derived from a multiple alignment of all the members of the family and contains the highest probability amino acid at each position. In the example below, the first line is the consensus, the second indicate matches and mismathces between the query sequence and the consensus, and the third indicates the query sequence. Capital letters in the consensus indicate highly conserved residues (>50% chance). In the second line, matches to the highest probability residue are indicated with the letter of the amino acid. +'s indicate a match to another amino acid that has a non-zero probability, and spaces indicate mismatches. In the query sequence, -'s indicate gaps in the sequence needed to make the alignment.
HMMER Feature Attributes
The following figure is a screen shot of the Methanosarcina acetivorans website showing feature details for a feature of type HMMER.
The attributes for a HMMER feature are:
- PFAM Name The description of the Pfam family or domain
- Family The Pfam name for the protein family or domain. In some cases, multiple families can exist for a given description (e.g. Transposases) where each Pfam family corresponds to a subfamily
- Accession The Pfam accession
- Score The score of the alignment
- Sequence The name of the sequence on which this feature has been called. In the example shown above, the gene was called before the contigs making up the assembly where combined into a single genome sequence.
- Start The start position of the feature on the sequence. Start is always less than stop.
- Stop The stop position of the feature on the sequence. Stop is always greater than start.
- Strand The strand on which the feature was called (+ or -).
- Expected The probability that this particular feature could have been predicted by chance
- HMM Start The amino acid start position relative to the consensus sequence of the HMM model for this alignment
- HMM Stop - The amino acid stop position relative to the consensus sequence of the HMM model for this alignment
- Hit Length - The length of the alignment in amino acids relative to the consensus sequence of the HMM model for this alignment
- Alignment The alignment between the tranlated Methanosarcina acetivorans sequence and the the consensus sequence of the HMM model
- Subtype The feature type.
- Feature ID An internal unique identifier for this gene. These identifiers should not be relied upon to identify genes outside of the community annotation project
- Sequence ID An internal unique identifier for this sequence. These identifiers should not be relied upon to identify sequences outside of the community annotation project
TRNAs
Description
Feaures of type TRNA are predicted transfer RNAs corresponding to the output of tRNAscan-SE (http://www.genetics.wustl.edu/eddy/tRNAscan-SE/). The annotation of Methanosarcina acetivoran used tRNAscan-SE version 1.12.
According to tRNAscan identifies 99-100% of true transfer RNAs when searching the Sprintzl tRNA database. In simulated and real genomic DNA, tRNAscan-SE has a false positive rate of less than 1 per 15 GB. Thus tRNAscan-SE is both a highly sensitive and specific tool for find transfer RNAs is the single tool used to annotate these features on the Methanosarcina acetivorans genome.
TRNA Feature Attributes
The following figure is a screen shot of the Methanosarcina acetivorans website showing feature details for a feature of type TRNA.
The attributes for a TRNA feature are:
- tRNA Name The name of the transfer RNA using amino acid abreviations
- Sequence The name of the sequence on which this feature has been called. In the example shown above, the gene was called before the contigs making up the assembly where combined into a single genome sequence.
- Start The start position of the feature on the sequence. Start is always less than stop.
- Stop The stop position of the feature on the sequence. Stop is always greater than start.
- Length The length of the feature on the Methanosarcina acetivorans genome
- Strand The strand on which the feature was called (+ or -).
- Subtype The feature type.
- Type The predicted amino acid charged to the transfer RNA using amino acid abbreviations. Potential tRNA pseudogenes are labeled "Psuedo".
- Anticodon The predicted anticodon for this tRNA
- Score the score of the predicted tRNA in bits. Only features with scores>20 bits are predicted to be tRNAs.
- Intron Begin The nucleotide start position of a predicted intron if any.
- Intron End - The nucleotide stop position of a predicted intron if any.
- Feature ID An internal unique identifier for this gene. These identifiers should not be relied upon to identify genes outside of the community annotation project
- Sequence ID An internal unique identifier for this sequence. These identifiers should not be relied upon to identify sequences outside of the community annotation project
Feature Search
Basic SearchingThe Basic Search is accessible via a Feature Search link in the top panel of the main website.
The drop-down menu on the left allows you to select the feature type, and the text-input field on the right allows you to enter search words.
- Matches will contain ALL words listed
- Search is NOT case-sensitive
- Word order does not matter unless the string has quotation marks, e.g. "pyruvate kinase"
- The symbol * or % will match any number of characters, e.g. *methyl*
Advanced Searching
Clicking on the Advanced Search link from the Basic Search page will allow you to search on additional fields such as location, EC Number, or protein category.
The search will find features that match ALL the specified fields. Changing the Feature Type via the drop-down menu in the upper left will change which search fields are available.
Search Results
The search will return a table containing the first 50 matches to your search query. Additional matches are accessible through the Prev and Next links listed below the results table.
- Links within the Search view allow you to connect to ExPASy, Sanger PFAM, and other external sites associated with the displayed information. Feature name links will display a page containing detailed feature information. The table column headers are links that will sort the results (Length, Hit Length, Score, and %ID sort in descending order, all others sort in ascending order).
To refine your search, you can use the Back button in your web browser or start a new search by clicking on the Search link in the left-hand side panel.
Detailed Feature Information
From the Search Results, you can view the detailed information associated with a feature by clicking on the feature name link.
Links within the Detailed Feature view allow you to connect to ExPASy, Kegg, Pfam and other external sites associated with the displayed information.The Search for Overlapping Features search allows you to retrieve features of another type that overlap the selected feature.
You may visually view the selected feature in either of two graphical tools:
- The Feature Map provides a quick view of this feature and all other overlapping features. The selected feature will be highlighted in the clickable-GIF image produced. This graphical tool is likely to be faster than the Genome Browser
- The Genome Browser offers a more navigable graphical view of the features in a particular region of the sequence. From the Genome Browser, you can scroll and zoom within the specified window on the sequence
These visualization tools are described in the next section.
Visualization Tools
Two methods are provided for visualizing the genome and its annotation:
- The Feature Map which is an image map based tool
- The Genome Browser which is a java applet based approach
Both tools provide a graphical display of features annotated on the genome and also offer clickable links to features on the genome. Which tool to used depends on the goal:
- The Feature Map is appropriate for quickly visualizing a region of the genome and its annotation. It is also appropriate for rapid visual scanning of the genome. It is provided for users with slower computers or network links. The Feature Map is image map based and therefore does not require computational power on the client computer.
- The Genome Broswer is appopriate for more detailed investigation of a region of the genome or for users with faster computers and network links. The Genome Browser is Java applet based and requires that the client browser have a Java Plugin (version 1.2 or later) installed to run. The Genome Browser supports more advanced capabilities for navigation and zooming as well as the ability to see the underlying genome sequence.
Feature Map
The Feature Map is an image map based application that presents a static clickable graphical representation of genetic features in a given stretch of sequence. It allows users obtain detailed information about individual features by clicking on them, and easily control which features in which stretches of segment are shown. Individual features of interest may be highlighted.
The Feature Map consists of two areas:
Feature Map Display
At the top of the screen is the name of the organism. The sequence identifier is shown as the selected item in a drop down menu below the map. The start and stop positions (in base pairs) of the selected subsequence are shown in text entry boxes next to the sequence selector. Pick a new sequence id or modify the stop or start value and then hit the Redraw button to focus in on a different stretch of sequence.
The features themselves are shown in the central Feature Display Panel. Different feature types are represented by different colors, described in the legend below the map. Overlapping features are pushed into two dimensions, with higher ranking features nearer the top of the map. Each feature is depicted as an arrow, the orientation of which indicates the strand on which the feature is found: right for positive, left for negative. If there is sufficient room, the name of each feature is shown on the map. Clicking a feature brings up a window containing detailed information about it. On maps with more that 2000 features these feature detail hyperlinks are deactivated, due to the amount of time it would take to download them. In this situation, users may zoom in or otherwise change their navigational criteria to reduce the number of features, or disregard the download time and download them anyway.
The feature map contains two rulers: the Local Region Ruler above the feature display region and the Global View Ruler below the feature panel. Each ruler has ten segments, measured in base pairs (BP), or thousand base pairs (KB) for sequences longer than 10,000 base pairs.
The Local Region Ruler measures the length of the displayed subsequence. Click anywhere on this ruler to re-center the image map.
The Global View Ruler spans the length of the entire parent sequence. The subsequence displayed in the Feature Display Panel is shown as a red box. Click anywhere on this ruler to reposition the image map.
Above the top ruler the Zoom Tool indicated by an image of a magnifying glass flanked by a plus and minus sign. Click on the plus sign to zoom in on the center of the current sequence. Click the minus sign to zoom out.
Navigation and Feature Selection Panel
Below the bottom ruler is a detailed Navigation Control Panel. The Next Window and Prev Window buttons caused the next or previous adjacent subsequence to be displayed. The start and stop text entry boxes, the sequence id selector, and the Redraw button, also located here, have already been described.
The lower segment of the navigational control panel contains the Feature Selection Panel.
A legend defining the colors used to indicate the different feature types also contains checkboxes which may be use to specify which feature types should be shown. Check the desired feature types and hit 'redraw.' All feature types are checked by default.
Features of type BLASTX and BLASTN tend to occur very frequently and there are often tens or even hundreds of them overlapping a single gene. Beyond a certain point these hits are often of less value. For both BLASTX and BLASTN, there are input fields for minimum required score and expected value. For BLASTX, a maximum number of top hits per gene may also be specified.
The Feature Map provides similar functionality to the Genome Browser. The Genome Browser , a Java applet, is better suited for extended study of larger sequences. Although slower to load initially, intra-sequence movement is much quicker once this initial penalty has been paid. The Feature Map, a server side web application, is better suited for quick snapshots of small subsequences.
Genome Browser
The genome browser is a tool to visualize a specific region of interest in the genome in a greater detail. The Genome Browser is Java applet based and requires that the client browser have a Java Plugin (version 1.2 or later) installed to run. The first time that the Genome browser is run during a netscape session, the java classes are loaded across the network.
The figure below shows a typical genome browser view. The browser opens in a new window. There are two major regions in the browser:
Feature Viewer
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The feature viewer consists of Arrow tool, Zoom tool, Feature display area and a Selected feature description area.
- Mouse Left click : Selects or deselects the feature. If a feature is selected, information about that feature is displayed in selected feature description area.
- Mouse Right click: brings up the pop up menu that shows various navigation options. Additionally if a feature is selected, a few more choices become available (Zoom to feature and center feature)
- Zoom In: Zooms in by a factor of 2, while trying to maintain the point of zoom to the center of the feature display area.
- Zoom Out: Zooms out by a factor of 2 until the whole 200000 base pair features are displayed, while trying to maintain the point of zoom to be the center of the feature display area.
- Zoom to Sequence: This is a specific zoom in so that the sequence ruler is visible.
- Zoom out fully: Shows the maximum possible feature display area for the selected region.
- Center point: Centers the feature display around the point
- Go to Sequence position: requests for an input from the user, checks if the position number given is within the bounds of the displayed sequence and displays that area if already not displayed..
- Zoom to feature: Allows the selected feature to be displayed covering the entire display area (zooming if necessary).
- Center Feature: Centers the selected feature.
- Zoom: can be accomplished by using the zoom in "+" and the "-" (zoom out) keys.
- Scrolling: can be controlled either by using PgUp/PgDn keys or up or down arrow keys. The PgUp/PgDn speed is twice as fast as that of the arrow keys.
- Mouse Left Click: Zooms in (if possible).
- Mouse Right Click: Zooms out (if possible).
Navigation in the Feature Viewer:
There are two modes of navigation in the feature display area: Arrow tool mode and Zoom tool mode:
Arrow tool: When clicked on this button the cursor shows up as an arrow in the feature display area. Within this mode you can perform the following functions:
Mouse Clicks
POP-UP Menu
Mouse Double-Click
In the arrow mode, if a feature (Blast or Hmmer ) is double-clicked, it opens another browser window with information link about that feature.
Key-board Shortcuts
Mouse over:
Mouse over in this mode shows the tool tip text if available.
Zoom tool: This mode of navigation is specifically designed for zooming in or out using the mouse clicks alone. Mouse Click: In this mode the mouse cursor looks like a magnifying glass. Zooming in can be achieved by using the left mouse button click, and zooming out can be achieved by using right mouse button click.
Mouse Hold, Drag and Release: In the zoom mode, one can zoom in to a region of display area by holding down the left mouse button and dragging it across the region of interest. When the mouse is released, the display will zoom in to the selected area.
The feature description box lies just below the feature display area. It shows a brief description of the selected feature.
Mouse over: Mouse over in this mode shows the tool tip text if available.
Feature Options Selector
- Consists of
- The Feature Coordinates Selector has the option of selecting the Sequence number, the start and the stop position in the sequence, moving from one window to the next adjacent window and of refreshing the feature display after modifying the feature options properties.
- The Feature Type Selection supports Gene, Glimmer, BlastX, BlastN, Hmmer and Trna types. The BlastX and BlastN can be performed with various scores and expected values. There is also a choice of number of BlastX hits displayed for optimal performance of the applet.
Miscellaneous
For additional help, check the FAQ or Contact Us.