How to run CD-HIT/Maketable5 on multiple FASTA files

If you have several accession numbers out of which you want to build a single database and run CD-HIT; this can be done using our BioTools Work Environment
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Semi-automated Genome Analysis (Ujjwal Kumar)

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Create a list of homologs from a sequence, accession or Gi number

The first step in most of your projects will be to collect a list of homologs. If you already have an accession number, sequence or Gi number, you are ready to start.

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Find out highlighted TMS regions in the sequence using HMMGAP

HMMGAP is a tool that is used within several other programs and can also be used as a standalone feature. HMMGAP takes two parameters: “Input Sequence” and “Gap Segment.” Gap Segment refers a segment of the input sequence containing gaps delimited with periods. HMMGAP returns the segment with highlighted putative TMS regions that are numbered relative to the entire sequence. The input segment does not have to contain gaps, but is usually determined by a Needleman Wunsch comparison.

HMMGAP can be accessed online here

To access the standalone version, type the following syntax in the terminal window

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Binary Alignments using GSAT

This tutorial will explain how to use GSAT to compare two sequences and retrieve a Standard Score in standard deviations. GSAT is newer replacement for the deprecated GAP program.

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