server/catgenome/src/main/resources/static/blastx.html [76:209]:
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<tr>
<td><strong><code>-max_intron_length</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments. Default = <code>0</code></td>
</tr>
<tr>
<td><strong><code>-matrix</code></strong></td>
<td>String</td>
<td>Scoring matrix name (normally <code>BLOSUM62</code>)</td>
</tr>
<tr>
<td><strong><code>-threshold</code></strong></td>
<td>Real, &gt;= 0</td>
<td>Minimum word score such that the word is added to the BLAST lookup table</td>
</tr>
<tr>
<td><strong><code>-comp_based_stats</code></strong></td>
<td>String</td>
<td>Use composition-based statistics:<br/><code>D</code> or <code>d</code>: default (equivalent to <code>2</code>)<br/><code>0</code> or <code>F</code> or <code>f</code>: No composition-based statistics<br/><code>1</code>: Composition-based statistics as in NAR 29:2994-3005, 2001<br/><code>2</code> or <code>T</code> or <code>t</code>: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties<br/><code>3</code>: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally.<br/>Default = <code>2</code></td>
</tr>
<tr>
<td><strong>Query filtering options</strong></td>
</tr>
<tr>
<td><strong><code>-seg</code></strong></td>
<td>String</td>
<td>Filter query sequence with SEG (Format: <code>yes</code>, <code>window locut hicut</code>, or <code>no</code> to disable). Default = <code>12 2.2 2.5</code></td>
</tr>
<tr>
<td><strong><code>-soft_masking</code></strong></td>
<td>Boolean</td>
<td>Apply filtering locations as soft masks. Default = <code>false</code></td>
</tr>
<tr>
<td><strong><code>-lcase_masking</code></strong></td>
<td>Flag</td>
<td>Use lower case filtering in query and subject sequence(s)?</td>
</tr>
<tr>
<td><strong>Restrict search or results</strong></td>
</tr>
<tr>
<td><strong><code>-db_soft_mask</code></strong></td>
<td>String</td>
<td>Filtering algorithm ID to apply to the BLAST database as soft masking. Incompatible with: <strong><code>-db_hard_mask</code></strong></td>
</tr>
<tr>
<td><strong><code>-db_hard_mask</code></strong></td>
<td>String</td>
<td>Filtering algorithm ID to apply to the BLAST database as hard masking. Incompatible with: <strong><code>-db_soft_mask</code></strong></td>
</tr>
<tr>
<td><strong><code>-qcov_hsp_perc</code></strong></td>
<td>Real, 0..100</td>
<td>Percent query coverage per hsp</td>
</tr>
<tr>
<td><strong><code>-max_hsps</code></strong></td>
<td>Integer, &gt;= 1</td>
<td>Set maximum number of HSPs per subject sequence to save for each query</td>
</tr>
<tr>
<td><strong><code>-culling_limit</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit. Incompatible with: <strong><code>-best_hit_overhang</code></strong>, <strong><code>-best_hit_score_edge</code></strong></td>
</tr>
<tr>
<td><strong><code>-best_hit_overhang</code></strong></td>
<td>Real, (&gt; 0 and &lt; 0.5)</td>
<td>Best Hit algorithm overhang value (recommended value: <code>0.1</code>). Incompatible with: <strong><code>-culling_limit</code></strong></td>
</tr>
<tr>
<td><strong><code>-best_hit_score_edge</code></strong></td>
<td>Real, (&gt; 0 and &lt; 0.5)</td>
<td>Best Hit algorithm score edge value (recommended value: <code>0.1</code>). Incompatible with: <strong><code>-culling_limit</code></strong></td>
</tr>
<tr>
<td><strong><code>-subject_besthit</code></strong></td>
<td>Flag</td>
<td>Turn on best hit per subject sequence</td>
</tr>
<tr>
<td><strong>Statistical options</strong></td>
</tr>
<tr>
<td><strong><code>-dbsize</code></strong></td>
<td>Integer</td>
<td>Effective length of the database</td>
</tr>
<tr>
<td><strong><code>-searchsp</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>Effective length of the search space</td>
</tr>
<tr>
<td><strong><code>-sum_stats</code></strong></td>
<td>Boolean</td>
<td>Use sum statistics</td>
</tr>
<tr>
<td><strong>Extension options</strong></td>
</tr>
<tr>
<td><strong><code>-xdrop_ungap</code></strong></td>
<td>Real</td>
<td>X-dropoff value (in bits) for ungapped extensions</td>
</tr>
<tr>
<td><strong><code>-xdrop_gap</code></strong></td>
<td>Real</td>
<td>X-dropoff value (in bits) for preliminary gapped extensions</td>
</tr>
<tr>
<td><strong><code>-xdrop_gap_final</code></strong></td>
<td>Real</td>
<td>X-dropoff value (in bits) for final gapped alignment</td>
</tr>
<tr>
<td><strong><code>-ungapped</code></strong></td>
<td>Flag</td>
<td>Perform ungapped alignment only?</td>
</tr>
<tr>
<td><strong><code>-window_size</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>Multiple hits window size, use <code>0</code> to specify 1-hit algorithm</td>
</tr>
<tr>
<td><strong>Miscellaneous options</strong></td>
</tr>
<tr>
<td><strong><code>-use_sw_tback</code></strong></td>
<td>Flag</td>
<td>Compute locally optimal Smith-Waterman alignments?</td>
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server/catgenome/src/main/resources/static/tblastn.html [71:204]:
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<tr>
<td><strong><code>-max_intron_length</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments. Default = <code>0</code></td>
</tr>
<tr>
<td><strong><code>-matrix</code></strong></td>
<td>String</td>
<td>Scoring matrix name (normally <code>BLOSUM62</code>)</td>
</tr>
<tr>
<td><strong><code>-threshold</code></strong></td>
<td>Real, &gt;= 0</td>
<td>Minimum word score such that the word is added to the BLAST lookup table</td>
</tr>
<tr>
<td><strong><code>-comp_based_stats</code></strong></td>
<td>String</td>
<td>Use composition-based statistics:<br/><code>D</code> or <code>d</code>: default (equivalent to <code>2</code>)<br/><code>0</code> or <code>F</code> or <code>f</code>: No composition-based statistics<br/><code>1</code>: Composition-based statistics as in NAR 29:2994-3005, 2001<br/><code>2</code> or <code>T</code> or <code>t</code>: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties<br/><code>3</code>: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally.<br/>Default = <code>2</code></td>
</tr>
<tr>
<td><strong>Query filtering options</strong></td>
</tr>
<tr>
<td><strong><code>-seg</code></strong></td>
<td>String</td>
<td>Filter query sequence with SEG (Format: <code>yes</code>, <code>window locut hicut</code>, or <code>no</code> to disable). Default = <code>12 2.2 2.5</code></td>
</tr>
<tr>
<td><strong><code>-soft_masking</code></strong></td>
<td>Boolean</td>
<td>Apply filtering locations as soft masks. Default = <code>false</code></td>
</tr>
<tr>
<td><strong><code>-lcase_masking</code></strong></td>
<td>Flag</td>
<td>Use lower case filtering in query and subject sequence(s)?</td>
</tr>
<tr>
<td><strong>Restrict search or results</strong></td>
</tr>
<tr>
<td><strong><code>-db_soft_mask</code></strong></td>
<td>String</td>
<td>Filtering algorithm ID to apply to the BLAST database as soft masking. Incompatible with: <strong><code>-db_hard_mask</code></strong></td>
</tr>
<tr>
<td><strong><code>-db_hard_mask</code></strong></td>
<td>String</td>
<td>Filtering algorithm ID to apply to the BLAST database as hard masking. Incompatible with: <strong><code>-db_soft_mask</code></strong></td>
</tr>
<tr>
<td><strong><code>-qcov_hsp_perc</code></strong></td>
<td>Real, 0..100</td>
<td>Percent query coverage per hsp</td>
</tr>
<tr>
<td><strong><code>-max_hsps</code></strong></td>
<td>Integer, &gt;= 1</td>
<td>Set maximum number of HSPs per subject sequence to save for each query</td>
</tr>
<tr>
<td><strong><code>-culling_limit</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit. Incompatible with: <strong><code>-best_hit_overhang</code></strong>, <strong><code>-best_hit_score_edge</code></strong></td>
</tr>
<tr>
<td><strong><code>-best_hit_overhang</code></strong></td>
<td>Real, (&gt; 0 and &lt; 0.5)</td>
<td>Best Hit algorithm overhang value (recommended value: <code>0.1</code>). Incompatible with: <strong><code>-culling_limit</code></strong></td>
</tr>
<tr>
<td><strong><code>-best_hit_score_edge</code></strong></td>
<td>Real, (&gt; 0 and &lt; 0.5)</td>
<td>Best Hit algorithm score edge value (recommended value: <code>0.1</code>). Incompatible with: <strong><code>-culling_limit</code></strong></td>
</tr>
<tr>
<td><strong><code>-subject_besthit</code></strong></td>
<td>Flag</td>
<td>Turn on best hit per subject sequence</td>
</tr>
<tr>
<td><strong>Statistical options</strong></td>
</tr>
<tr>
<td><strong><code>-dbsize</code></strong></td>
<td>Integer</td>
<td>Effective length of the database</td>
</tr>
<tr>
<td><strong><code>-searchsp</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>Effective length of the search space</td>
</tr>
<tr>
<td><strong><code>-sum_stats</code></strong></td>
<td>Boolean</td>
<td>Use sum statistics</td>
</tr>
<tr>
<td><strong>Extension options</strong></td>
</tr>
<tr>
<td><strong><code>-xdrop_ungap</code></strong></td>
<td>Real</td>
<td>X-dropoff value (in bits) for ungapped extensions</td>
</tr>
<tr>
<td><strong><code>-xdrop_gap</code></strong></td>
<td>Real</td>
<td>X-dropoff value (in bits) for preliminary gapped extensions</td>
</tr>
<tr>
<td><strong><code>-xdrop_gap_final</code></strong></td>
<td>Real</td>
<td>X-dropoff value (in bits) for final gapped alignment</td>
</tr>
<tr>
<td><strong><code>-ungapped</code></strong></td>
<td>Flag</td>
<td>Perform ungapped alignment only?</td>
</tr>
<tr>
<td><strong><code>-window_size</code></strong></td>
<td>Integer, &gt;= 0</td>
<td>Multiple hits window size, use <code>0</code> to specify 1-hit algorithm</td>
</tr>
<tr>
<td><strong>Miscellaneous options</strong></td>
</tr>
<tr>
<td><strong><code>-use_sw_tback</code></strong></td>
<td>Flag</td>
<td>Compute locally optimal Smith-Waterman alignments?</td>
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