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NIH GCG-FAQ
TABLE of CONTENTS

Introduction | Connecting | Graphics | Printing | GCG Programs | Assistance
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Searches can be single words - phrases,placed within quotes(") - or multiple words separated by boolean operators (and/or/not)
Introduction
  1. What do I need to use GCG at NIH?
  2. How do I use GCG from a Mac?
  3. How do I use GCG from a PC?
  4. How do I use GCG from a Unix machine?
  5. Cursor (arrow) keys don't work (in Seqed / Geledit).
  6. Delete and backspace keys don't work in Seqed.
  7. What X-terminal emulators can I use on a Mac or PC?
  8. How do I get GCG graphics on my Mac?
  9. How do I get GCG graphics on my PC (clone)?
  10. How do I get GCG graphics on my Unix workstation?
  11. How do I get graphics on my Windows NT machine?
  12. What if my connection software can't do graphics?
  13. How can I modify a GCG graphics figure for publication?
  14. How do I know if my setup can display GCG graphics?
  15. What do I do with a figure file?
  16. How can I learn to use GCG?
  17. Where do I get GCG manuals?
  18. I have a GCG question; who do I ask?
  19. What GCG program should I use for?
  20. What other online help or GCG FAQs are out there?
  21. How do I print to my local (non-networked) printer?
  22. How can I print to my network printer?
  23. Can I print from helix to an AppleTalk printer?
  24. Can I print from helix to a printer that is attached directly to my PC/Mac ?
  25. My printer's currently dead; where can I print?
  26. How do I print GCG graphics to my postscript printer?
  27. How do I print GCG graphics to my HP plotter or printer?
  28. What if my printer can't do postscript?
  29. My printer prints black-and-white but I need color prints.
  30. How do I know what port my LaserWriter is connected to?
  31. GCG doesn't accept my sequence data format.
  32. How do I save scores from Pileup runs ?
  33. How do I save the genetic distance scale from Growtree ?
  34. I keep getting files called seqed.log in my directory.
  35. Seqed says 'recovering...' for ever!
  36. What databases are available for Fasta searches?
  37. How do I get information about the databases?
  38. Motifs doesn't find a known motif in my protein.
  39. What databases are available for Blast searches?
  40. Fasta says "No sequences to compare to query sequence!"
  41. Reformat gave me an empty file.
  42. Reformat put the header into the sequence.
  43. Where do I get the codon usage table for xxx?
  44. What options are available with each program?
  45. How do I edit more than 30 aligned sequences?
  46. Why can't I find a published sequence?
  47. How do I get my sequences into Pileup?
  48. Should I use Blast or Fasta?
  49. Can I use Fasta with a short sequence?
  50. Should I use framesearch or Blastx?
  51. After a Pileup run, how do I calculate a consensus sequence?
  52. How can I put a Pretty consensus output into other GCG programs?
  53. Can I change how matches are displayed in Pretty?
  54. How do I import a sequence file into GCG?
  55. Reformat cut off the end of my sequence.
  56. How do I translate the coding regions of a Genbank entry?
  57. How do I stop Fasta?
  58. When should I use stringsearch?
  59. How can I get a tfasta output aligned with Pileup?
  60. How do I design a primer?
  61. How do I convert peptide sequences from 1-letter to 3-letter amino acid codes? -
  62. Blast error: Server did not say ok
  63. Why have my alignments changed in Version 9?
  64. Pileup doesn't find conserved motifs in my alignment in Version 9
  65. How do I run blast searches in batch mode?
  66. How do I view the trees from Paupsearch?
  67. How do I search a complete genome?
  68. How do I kill a paupsearch run?
  69. How can I find all relevant sequences with Lookup?
  70. How can I find bases 3134678 to 3136537 of the E. Coli genome?
  71. How can I search for promoter regions?
  72. What is a FAQ?
  73. What is GCG?
  74. What is helix?
  75. What is GCG-Lite?
  76. How do I edit my files on helix?
  77. What shell should I use on helix?
  78. I don't know any Unix!
  79. How do I cite the GCG package?
  80. (VAX) VMS to Unix issues

Connecting
  1. What do I need to use GCG at NIH?
  2. How do I use GCG from a Mac?
  3. How do I use GCG from a PC?
  4. How do I use GCG from a Unix machine?
  5. Cursor (arrow) keys don't work (in Seqed / Geledit).
  6. Delete and backspace keys don't work in Seqed.
  7. What X-terminal emulators can I use on a Mac or PC?
  8. How do I get GCG graphics on my Mac?
  9. How do I get GCG graphics on my PC (clone)?
  10. How do I get GCG graphics on my Unix workstation?
  11. How do I get graphics on my Windows NT machine?
  12. What if my connection software can't do graphics?
  13. How can I modify a GCG graphics figure for publication?
  14. How do I know if my setup can display GCG graphics?
  15. What do I do with a figure file?
  16. How can I learn to use GCG?
  17. Where do I get GCG manuals?
  18. I have a GCG question; who do I ask?
  19. What GCG program should I use for?
  20. What other online help or GCG FAQs are out there?
  21. How do I print to my local (non-networked) printer?
  22. How can I print to my network printer?
  23. Can I print from helix to an AppleTalk printer?
  24. Can I print from helix to a printer that is attached directly to my PC/Mac ?
  25. My printer's currently dead; where can I print?
  26. How do I print GCG graphics to my postscript printer?
  27. How do I print GCG graphics to my HP plotter or printer?
  28. What if my printer can't do postscript?
  29. My printer prints black-and-white but I need color prints.
  30. How do I know what port my LaserWriter is connected to?
  31. GCG doesn't accept my sequence data format.
  32. How do I save scores from Pileup runs ?
  33. How do I save the genetic distance scale from Growtree ?
  34. I keep getting files called seqed.log in my directory.
  35. Seqed says 'recovering...' for ever!
  36. What databases are available for Fasta searches?
  37. How do I get information about the databases?
  38. Motifs doesn't find a known motif in my protein.
  39. What databases are available for Blast searches?
  40. Fasta says "No sequences to compare to query sequence!"
  41. Reformat gave me an empty file.
  42. Reformat put the header into the sequence.
  43. Where do I get the codon usage table for xxx?
  44. What options are available with each program?
  45. How do I edit more than 30 aligned sequences?
  46. Why can't I find a published sequence?
  47. How do I get my sequences into Pileup?
  48. Should I use Blast or Fasta?
  49. Can I use Fasta with a short sequence?
  50. Should I use framesearch or Blastx?
  51. After a Pileup run, how do I calculate a consensus sequence?
  52. How can I put a Pretty consensus output into other GCG programs?
  53. Can I change how matches are displayed in Pretty?
  54. How do I import a sequence file into GCG?
  55. Reformat cut off the end of my sequence.
  56. How do I translate the coding regions of a Genbank entry?
  57. How do I stop Fasta?
  58. When should I use stringsearch?
  59. How can I get a tfasta output aligned with Pileup?
  60. How do I design a primer?
  61. How do I convert peptide sequences from 1-letter to 3-letter amino acid codes? -
  62. Blast error: Server did not say ok
  63. Why have my alignments changed in Version 9?
  64. Pileup doesn't find conserved motifs in my alignment in Version 9
  65. How do I run blast searches in batch mode?
  66. How do I view the trees from Paupsearch?
  67. How do I search a complete genome?
  68. How do I kill a paupsearch run?
  69. How can I find all relevant sequences with Lookup?
  70. How can I find bases 3134678 to 3136537 of the E. Coli genome?
  71. How can I search for promoter regions?

Graphics
  1. How do I get GCG graphics on my Mac?
  2. How do I get GCG graphics on my PC (clone)?
  3. How do I get GCG graphics on my Unix workstation?
  4. How do I get graphics on my Windows NT machine?
  5. What if my connection software can't do graphics?
  6. How can I modify a GCG graphics figure for publication?
  7. How do I know if my setup can display GCG graphics?
  8. What do I do with a figure file?
  9. How can I learn to use GCG?
  10. Where do I get GCG manuals?
  11. I have a GCG question; who do I ask?
  12. What GCG program should I use for?
  13. What other online help or GCG FAQs are out there?
  14. How do I print to my local (non-networked) printer?
  15. How can I print to my network printer?
  16. Can I print from helix to an AppleTalk printer?
  17. Can I print from helix to a printer that is attached directly to my PC/Mac ?
  18. My printer's currently dead; where can I print?
  19. How do I print GCG graphics to my postscript printer?
  20. How do I print GCG graphics to my HP plotter or printer?
  21. What if my printer can't do postscript?
  22. My printer prints black-and-white but I need color prints.
  23. How do I know what port my LaserWriter is connected to?
  24. GCG doesn't accept my sequence data format.
  25. How do I save scores from Pileup runs ?
  26. How do I save the genetic distance scale from Growtree ?
  27. I keep getting files called seqed.log in my directory.
  28. Seqed says 'recovering...' for ever!
  29. What databases are available for Fasta searches?
  30. How do I get information about the databases?
  31. Motifs doesn't find a known motif in my protein.
  32. What databases are available for Blast searches?
  33. Fasta says "No sequences to compare to query sequence!"
  34. Reformat gave me an empty file.
  35. Reformat put the header into the sequence.
  36. Where do I get the codon usage table for xxx?
  37. What options are available with each program?
  38. How do I edit more than 30 aligned sequences?
  39. Why can't I find a published sequence?
  40. How do I get my sequences into Pileup?
  41. Should I use Blast or Fasta?
  42. Can I use Fasta with a short sequence?
  43. Should I use framesearch or Blastx?
  44. After a Pileup run, how do I calculate a consensus sequence?
  45. How can I put a Pretty consensus output into other GCG programs?
  46. Can I change how matches are displayed in Pretty?
  47. How do I import a sequence file into GCG?
  48. Reformat cut off the end of my sequence.
  49. How do I translate the coding regions of a Genbank entry?
  50. How do I stop Fasta?
  51. When should I use stringsearch?
  52. How can I get a tfasta output aligned with Pileup?
  53. How do I design a primer?
  54. How do I convert peptide sequences from 1-letter to 3-letter amino acid codes? -
  55. Blast error: Server did not say ok
  56. Why have my alignments changed in Version 9?
  57. Pileup doesn't find conserved motifs in my alignment in Version 9
  58. How do I run blast searches in batch mode?
  59. How do I view the trees from Paupsearch?
  60. How do I search a complete genome?
  61. How do I kill a paupsearch run?
  62. How can I find all relevant sequences with Lookup?
  63. How can I find bases 3134678 to 3136537 of the E. Coli genome?
  64. How can I search for promoter regions?

Printing
  1. How can I learn to use GCG?
  2. Where do I get GCG manuals?
  3. I have a GCG question; who do I ask?
  4. What GCG program should I use for?
  5. What other online help or GCG FAQs are out there?
  6. How do I print to my local (non-networked) printer?
  7. How can I print to my network printer?
  8. Can I print from helix to an AppleTalk printer?
  9. Can I print from helix to a printer that is attached directly to my PC/Mac ?
  10. My printer's currently dead; where can I print?
  11. How do I print GCG graphics to my postscript printer?
  12. How do I print GCG graphics to my HP plotter or printer?
  13. What if my printer can't do postscript?
  14. My printer prints black-and-white but I need color prints.
  15. How do I know what port my LaserWriter is connected to?
  16. GCG doesn't accept my sequence data format.
  17. How do I save scores from Pileup runs ?
  18. How do I save the genetic distance scale from Growtree ?
  19. I keep getting files called seqed.log in my directory.
  20. Seqed says 'recovering...' for ever!
  21. What databases are available for Fasta searches?
  22. How do I get information about the databases?
  23. Motifs doesn't find a known motif in my protein.
  24. What databases are available for Blast searches?
  25. Fasta says "No sequences to compare to query sequence!"
  26. Reformat gave me an empty file.
  27. Reformat put the header into the sequence.
  28. Where do I get the codon usage table for xxx?
  29. What options are available with each program?
  30. How do I edit more than 30 aligned sequences?
  31. Why can't I find a published sequence?
  32. How do I get my sequences into Pileup?
  33. Should I use Blast or Fasta?
  34. Can I use Fasta with a short sequence?
  35. Should I use framesearch or Blastx?
  36. After a Pileup run, how do I calculate a consensus sequence?
  37. How can I put a Pretty consensus output into other GCG programs?
  38. Can I change how matches are displayed in Pretty?
  39. How do I import a sequence file into GCG?
  40. Reformat cut off the end of my sequence.
  41. How do I translate the coding regions of a Genbank entry?
  42. How do I stop Fasta?
  43. When should I use stringsearch?
  44. How can I get a tfasta output aligned with Pileup?
  45. How do I design a primer?
  46. How do I convert peptide sequences from 1-letter to 3-letter amino acid codes? -
  47. Blast error: Server did not say ok
  48. Why have my alignments changed in Version 9?
  49. Pileup doesn't find conserved motifs in my alignment in Version 9
  50. How do I run blast searches in batch mode?
  51. How do I view the trees from Paupsearch?
  52. How do I search a complete genome?
  53. How do I kill a paupsearch run?
  54. How can I find all relevant sequences with Lookup?
  55. How can I find bases 3134678 to 3136537 of the E. Coli genome?
  56. How can I search for promoter regions?

GCG Programs
  1. How can I learn to use GCG?
  2. Where do I get GCG manuals?
  3. I have a GCG question; who do I ask?
  4. What GCG program should I use for?
  5. What other online help or GCG FAQs are out there?
  6. GCG doesn't accept my sequence data format.
  7. How do I save scores from Pileup runs ?
  8. How do I save the genetic distance scale from Growtree ?
  9. I keep getting files called seqed.log in my directory.
  10. Seqed says 'recovering...' for ever!
  11. What databases are available for Fasta searches?
  12. How do I get information about the databases?
  13. Motifs doesn't find a known motif in my protein.
  14. What databases are available for Blast searches?
  15. Fasta says "No sequences to compare to query sequence!"
  16. Reformat gave me an empty file.
  17. Reformat put the header into the sequence.
  18. Where do I get the codon usage table for xxx?
  19. What options are available with each program?
  20. How do I edit more than 30 aligned sequences?
  21. Why can't I find a published sequence?
  22. How do I get my sequences into Pileup?
  23. Should I use Blast or Fasta?
  24. Can I use Fasta with a short sequence?
  25. Should I use framesearch or Blastx?
  26. After a Pileup run, how do I calculate a consensus sequence?
  27. How can I put a Pretty consensus output into other GCG programs?
  28. Can I change how matches are displayed in Pretty?
  29. How do I import a sequence file into GCG?
  30. Reformat cut off the end of my sequence.
  31. How do I translate the coding regions of a Genbank entry?
  32. How do I stop Fasta?
  33. When should I use stringsearch?
  34. How can I get a tfasta output aligned with Pileup?
  35. How do I design a primer?
  36. How do I convert peptide sequences from 1-letter to 3-letter amino acid codes? -
  37. Blast error: Server did not say ok
  38. Why have my alignments changed in Version 9?
  39. Pileup doesn't find conserved motifs in my alignment in Version 9
  40. How do I run blast searches in batch mode?
  41. How do I view the trees from Paupsearch?
  42. How do I search a complete genome?
  43. How do I kill a paupsearch run?
  44. How can I find all relevant sequences with Lookup?
  45. How can I find bases 3134678 to 3136537 of the E. Coli genome?
  46. How can I search for promoter regions?

Assistance
  1. How can I learn to use GCG?
  2. Where do I get GCG manuals?
  3. I have a GCG question; who do I ask?
  4. What GCG program should I use for?
  5. What other online help or GCG FAQs are out there?

Comments and suggestions about this FAQ should be mailed to:
susanc@helix.nih.gov (Susan Chacko)

Last Updated: March 27, 2002